Upon exiting the college ranks at Stanford, Harbaugh took over as the Niners' sideline boss in 2011 and immediately guided his new club to its first playoff appearance and NFC West title since 2002. That campaign ended with a loss to the New York Giants in the conference championship game, but San Francisco took the next step a season ago by reaching Super Bowl XLVII.
Though San Francisco was in it until the end thanks to a spirited second-half comeback, the franchise ultimately fell short against the Baltimore Ravens, who are coached by Jim's older brother John.
Harbaugh has a good chance at following his sibling with a title of his own this season, though returning to the Super Bowl is never an easy task. The challenge will be erasing the memory of being so close to a title before coming up short.
"(I'm a) firm believer that if you have to talk about what you did yesterday, no matter how good it was, then you haven't done much today," noted Harbaugh as training camp began. "So, that's where we're at today going forward, trying to achieve things today."
It helps that the 49ers return the bulk of a defense that was one of the best in the NFL a season ago and now have a quarterback in Colin Kaepernick who is capable of making the big plays that the offense had lacked in previous years.
Kaepernick, a second-round selection in 2011, took over the starting job in Week 11 after Alex Smith suffered a concussion and played well enough that Harbaugh decided to stick with him under center, even after Smith was healthy. It ended up the right move for Harbaugh and the franchise, with the offense quickly melding with the quarterback.
"Kap is a diverse guy. And the coaches love him, the players love him," said Harbaugh. "It's unique in that way, maybe, for a quarterback. You don't always see that, but I see that with Kap. He's universally respected in the locker room and loved by his teammates."
Looking to give Kaepernick some help, the 49ers traded for wide receiver Anquan Boldin, who was fresh off of winning a championship with the Ravens. They had hoped to team him with Michael Crabtree to give the club a dangerous threat at wideout, but those plans are on hold for the foreseeable future thanks to a torn Achilles Crabtree suffered during organized team activities in late May.
Boldin was acquired in a trade on the same day that San Francisco dealt Smith, the top pick of the 2005 draft by the franchise, to Kansas City, making the full transition to Kaepernick complete.
In addition to filling out the offense, San Francisco also addressed perhaps its one weakness that doomed the club a season ago: the secondary. While the 49ers ranked second in total points allowed and third in total defense, and was one of only two teams to rank in the top five in all four defensive categories, the Niners' defensive backs struggled to contain big plays and talented quarterbacks all throughout the playoffs.
The likes of Aaron Rodgers, Matt Ryan and Joe Flacco all had their way with the secondary in the postseason and Boldin himself went for over 100 yards receiving with a touchdown in the Super Bowl.
Now he'll look to get his new club back to the big show with a different result.
2012 RECORD: 11-4-1 (1st, NFC West)
LAST PLAYOFF APPEARANCE: 2012, lost to Baltimore Ravens in Super Bowl XLVII
HEAD COACH (RECORD): Jim Harbaugh (24-7-1 in two seasons)
OFFENSIVE COORDINATOR: Greg Roman (third season with 49ers)
DEFENSIVE COORDINATOR: Vic Fangio (third season with 49ers)
KEY ADDITIONS: QB Colt McCoy (from Browns), WR Anquan Boldin (from Ravens), WR Marlon Moore (from Dolphins), WR Austin Collie (from Colts), TE Vance McDonald (2nd round, Rice), OG Adam Snyder, DE Glenn Dorsey (from Chiefs), DE Tank Carradine (2nd round, Florida State), CB Nnamdi Asomugha (from Eagles), CB Eric Wright (from Buccaneers), S Craig Dahl (from Rams), S Eric Reid (1st round, LSU), K Phil Dawson (from Browns)
KEY DEPARTURES: QB Alex Smith (to Chiefs), WR Randy Moss (free agent), WR Ted Ginn (to Panthers), TE Delanie Walker (to Titans), OG Leonard Davis (free agent), DT Ricky Jean Francois (to Colts), NT Isaac Sopoaga (to Eagles), LB Tavares Gooden (free agent), LB Larry Grant (free agent), LB Clark Haggans (free agent), S Dashon Goldson (to Buccaneers), K David Akers (to Lions)
QB: Kaepernick (1,814 passing yards, 10 TD, 3 INT in 2011) used a combination of his arm and feet to transform the club's offense. While his completion percentage and quarterback rating were lower than Smith in the regular season, he added another wrinkle to the scheme and added five rushing touchdowns.
And while Smith was consistent, his play-it-safe style with the offense was put to shame with the emergence of Kaepernick, who had 21 completions of 25- plus yards, a total that ranked second in the NFL in the span when he became a starter. He also set an NFL single-game playoff record by a quarterback with 181 yards versus Green Bay in the divisional round and also threw for over 300 yards in the Super Bowl.
The big question is how Kaepernick will respond to a full 16-game schedule, but offensive coordinator Greg Roman has already seen improvement.
"I think Colin's getting better, really at everything he does just because of the approach he takes. And he's definitely somebody with a live arm and I think he's really focused on all his throws: short, intermediate and deep," noted Roman during camp.
Things do get a little dicey for the Niners after that. With Smith gone, San Francisco traded for former Cleveland Browns quarterback Colt McCoy, who made 22 starts over his first two NFL seasons before appearing in just three games of relief a season ago. He has nearly as many career interceptions (20) as touchdown passes (21).
Harbaugh has an interesting choice for his third quarterback. He can either go with the more accurate and steady Scott Tolzien or roll the dice with rookie quarterback B.J. Daniels, who has a style closer to Kaepernick's.
RB: A presence in the Niners' backfield since 2005, Frank Gore is coming off his fourth Pro Bowl appearance after running for 1,214 yards on 258 carries a season ago.
The 2013 season may have a different look for Gore, the franchise's all-time leader in rushing yards, rushing touchdowns and carries. With Kaepernick's ability to throw downfield or keep the ball himself, Gore will continue to adjust to a read option.
"After playing the playoffs and seeing how easy you can get yards in the read option, I don't care what (the play) is," said the 30-year-old Gore, who managed 319 rushing yards and four touchdowns in the postseason. "It could be read option or other plays, as long as we get great plays from it, (the coaches) can call whatever."
San Francisco has a plethora of options behind Gore to keep the veteran fresh. Kendall Hunter saw the bulk of the reserve work before suffering a season- ending Achilles injury in Week 12, while LaMichael James and Anthony Dixon combined for 48 carries a season ago.
San Francisco also used a fourth-round pick on Marcus Lattimore out of South Carolina, but a knee injury that caused him to fall in the draft will slow down his journey to the NFL and it is possible he won't see action at all this year.
Third-year fullback Brad Miller paves the way for a running back group that has injury concerns.
WR: Crabtree (85 receptions, 1,105 receiving yards, 9 TD) had the breakout season the Niners had been waiting for since they took him 10th overall in the 2009 draft and really had an impact after Kaepernick became the starter.
San Francisco won't get to see the duo click over a full season thanks to Crabtree's injury, which the Niners hope is not season-ending, and Mario Manningham, second on the club a season ago with 42 catches, is also coming off multiple knee surgeries.
It's a good thing that the 49ers swung a deal to get the 32-year-old Boldin, a 6-foot-1 possession receiver who is a three-time Pro Bowler. He'll have a lot of pressure on him early due to injuries.
While there should be no worries with Boldin (65 receptions, 921 yards, 4 TD with Ravens), there is questionable depth after him. The biggest opportunity belongs to second-year wideout A.J. Jenkins, who has the speed to stretch Kaepernick's arm but went without a catch as a rookie.
Others expected to fill in until Manningham and Crabtree return include Kyle Williams (14 receptions, 1 TD), Marlon Moore (6 receptions, 1 TD with Dolphins), Austin Collie and rookie Quinton Patton.
TE: Though Vernon Davis' numbers have gone down since reaching nearly 1,000 yards receiving in both 2009 and '10, he remains a leader and could be a piece that helps fill the void at wide receiver.
The 6-foot-3, 250-pounder has the hands and speed to handle the position and seemed to finally click with Kaepernick during the postseason. A former strong supporter of Alex Smith, Davis is willing to help the team wherever possible.
"I'm willing to step up and do whatever they ask me to do, and they've been having me work with the wide receivers, line up at wide receiver, pretty much all over the place," noted Davis, who added it helps his feet and route running improve.
Of course, if Davis is to line up as a receiver from time to time, rookie Vance McDonald and Garrett Celek will need to step up at the tight end spot. The Niners grabbed McDonald out of Rice with a second-round pick and he can also line up all over the field, while Celek played in 13 games as a rookie last year.
OL: While San Francisco's offense is full of playmakers, its biggest strength is an offensive line that was one of just three units last year to have the same starting five in every game.
Left tackle Joe Staley was named a starter for a second straight Pro Bowl, with 2010 first-round draft picks Mike Iupati (left guard) and Anthony Davis (right tackle) two of just four members of that draft class to start every game between 2010-12. Iupati was a 2012 Pro Bowler, while Davis signed an extension through 2019.
Center Jonathan Goodwin is also a former Pro Bowl selection and right guard Alex Boone is a solid part of the line that will be tested with Kaepernick's mobility.
San Francisco added a versatile backup in Adam Snyder, who can play all five positions on the line. Daniel Kilgore and Joe Looney are among those who hit the field in jumbo formations.
DL: Though an elbow injury caused Justin Smith (66 tackles, 3 sacks) to miss the final two games of the regular season last year and snap his string of 185 straight starts, the Niners still felt the 33-year-old has something left in the motor and signed the end to a two-year extension through 2015.
Smith's ability to go full speed on every play takes some pressure off fellow end Ray McDonald (38 tackles, 2.5 sacks) and the duo will have a new nose tackle between them following the loss of Isaac Sopoaga in free agency. The Niners addressed the loss by signing former Kansas City Chief Glenn Dorsey to compete with Ian Williams.
San Francisco further added depth by selecting defensive end Tank Carradine in the second round from Florida State, though he is coming off an ACL injury.
LB: There is perhaps no better unit in football than the linebacking group that the 49ers put out on the football field. It starts in the middle with the outstanding duo of Patrick Willis and NaVorro Bowman and extends on the outside to Aldon Smith and Ahmad Brooks.
Willis, who suffered a broken hand during training camp, is just the 17th player in league history to make six straight Pro Bowls to begin a career and has posted over 100 tackles in five of his six seasons. He made 120 stops last year and has logged 17 1/2 sacks and seven interceptions over his career.
Bowman, though, is pushing his teammate as the best linebacker in football. Signed through 2018, he led the 49ers with 148 tackles and is joining Willis as a team leader despite entering just his fourth season.
While the inside backs chase down ball carriers and receivers, Aldon Smith wrecked havoc on the backfield as a sophomore in 2012. He challenged the single-season sack record before a nagging shoulder injury helped to prevent him from logging a sack over the final three games of the campaign. But he still finished with a franchise-record 19 1/2 sacks on the year and broke Reggie White's league record for most sacks over the first two seasons of a career with 33 1/2.
A healthy Smith could be a force again in 2013.
"I didn't get a chance to really heal up, but I've had this offseason and I've done a lot to get back to where I was and get better," he said.
Brooks added 6 1/2 sacks a season ago and San Francisco added a pair of rookies to the reserve group in Corey Lemonier and Nick Moody along with veteran Parys Haralson.
DB: The biggest change for the 49ers in the secondary is the loss of Pro Bowl free safety Dashon Goldson (69 tackles, 3 INT), who led the team in interceptions and signed with Tampa Bay in the offseason. That could be a good thing for the Niners in the long term once 2013 first-round pick Eric Reid blooms into the position.
San Francisco traded up 13 spots to nab Reid, a hard-hitter with better movement than Goldson. He could open the season as the starter next to strong safety Donte Whitner (83 tackles, 1 INT) if he holds off the returning C.J. Spillman and free agent signee Craig Dahl (78 tackles, 1 INT with Rams).
The safety position will be the last line of defense behind a shaky group of corners, a thin unit that took a hit during camp when Chris Culliver suffered a torn ACL that will keep him out for the season.
"It hurts, not only him, but it hurts the team," said veteran corner Carlos Rogers (56 tackles, 1 sack, 1 INT), who returns to start alongside Tarell Brown (57 tackles, 2 INT).
Tramaine Brock has the inside track at taking over Culliver's spot as the third corner, with Nnamdi Asomugha also in the mix after signing a one-year deal. Asomugha is coming off two disappointing seasons with the Philadelphia Eagles after emerging as one of the top corners in the game during his time with Oakland.
"We didn't really know what we were getting when we got Nnamdi," said 49ers defensive coordinator Vic Fangio. "He's had some good days (in camp) and some days where you weren't sure if he was going to still have it. I think we're kind of in between with him right now. Hopefully he'll be able to still have some gas left in his tank to go out there and play like he did prior to going to Philadelphia."
Just in case, the 49ers signed cornerback Eric Wright, who they tried to acquire in a trade with the Buccaneers before he failed a physical. He was released and signed a one-year deal with San Francisco as he joins his fourth team in four years.
SPECIAL TEAMS: The 49ers feature two Pro Bowl legs in punter Andy Lee and first-year Niner Phil Dawson.
Lee has consistently been one of the top punters in the game and made the Pro Bowl last year. He led the league with a 43.2 net punting average last year and stuck 36 of his kicks inside the 20-yard line.
Lee has been with the 49ers since 2004 and has spent that entire time working with long snapper Brian Jennings, who is in his 14th season and is solid.
Dawson, meanwhile, replaces the inconsistent David Akers and enters his 15th season off his first Pro Bowl selection. Dawson hit on a career-best 93.5 percent of his field goals last year with Cleveland.
With Ted Ginn out of the mix, return duties fall to James and Kyle Williams.
COACHING: Harbaugh is just the eighth coach in NFL history to win a division title in each of his first two seasons and the third to claim consecutive division crowns after taking over a team with a losing record.
Though not always telling with the media, Harbaugh has gotten the respect of his players rather quickly in his time with the Niners and somehow prevented his move from Smith to Kaepernick from becoming an issue in the locker room.
THE SKINNY: It's never easy to get back to the top of the mountain and the 49ers will face increased competition, starting from within their own division.
"Our main goal is to get better this training camp, be better than last year," said Gore. "Win the first game, win the division and all is right. You win the division and everything will take care of itself."
Though the secondary still has big questions, the 49ers are really good where it matters: an excellent front seven on defense and a solid offensive line. Mix in a full season with Kaepernick and the defensive group won't be counted on to win as many games on its own as years past.
It all starts with Harbaugh making sure his team believes it got better.
"Knowing what it takes to get to where we got last year, we know if we want to get back there we've got to do better this year to win it," said Gore. "Kap's going to start from the jump leading the offense and our defense is going to be what they always do. I think we got better."