SAN FRANCISCO — Jim Harbaugh coaching Peyton Manning: In the Bay Area, fans of the San Francisco 49ers are beginning to think about the possibility and believe it might happen.

A former pro quarterback, Harbaugh worked wonders with Alex Smith in a matter of months for the NFC West champions, and signs point to the 49ers being a serious player in the Manning sweepstakes. Smith, who had a three-year offer to return to San Francisco, traveled to Miami on Sunday and met with Dolphins officials for 5 ½ hours.

If San Francisco doesn’t sign four-time league most valuable player Manning, the team could have some serious relationship-building to do with Smith even though he is close to Harbaugh.

There could be similar fallout in Tennessee and Denver if those suitors don’t land Manning, who turns 36 Saturday. Manning sat out the 2011 season because of neck problems and is trying to come back after he was released by Indianapolis.

Smith, 27, and Manning — who is weighing options — are both represented by agent Tom Condon.

“This is the NFL. I guess nothing surprises me anymore,” Smith told the South Florida Sun-Sentinel upon arriving at the airport. “I never thought a year ago (Peyton) Manning would be a free agent, either. I’m never surprised by anything.”

Unlike Tennessee and Denver, the 49ers have yet to publicly acknowledge interest in Manning.

MIAMI (AP) — San Francisco 49ers free agent quarterback Alex Smith is meeting with the Miami Dolphins, which could affect the Peyton Manning sweepstakes.

The 49ers are among three finalists for Manning, along with the Denver Broncos and Tennessee Titans.

A person familiar with the negotiations confirmed to The Associated Press that Smith was meeting with the Dolphins. The person spoke to the AP on condition of anonymity because the team has not publicly discussed Sunday’s meeting.

The 49ers had been working to re-sign Smith, the No. 1 overall 2005 draft pick who enjoyed his best season in 2011 under first-year 49ers coach Harbaugh, a former NFL quarterback. Smith and Manning have the same agent, Tom Condon.

The Dolphins‘ unexpected courtship of Smith came after they were spurned by Manning and then hosted former Green Bay Packers backup quarterback Matt Flynn for a weekend Saturday.

It was unclear whether the Dolphins expanded their quarterback search in a bid to pressure Flynn to sign soon. He visited the Seattle Seahawks earlier in the week.

Flynn left South Florida on Sunday morning, but a deal with the Dolphins remained a possibility, said his father, Alvin.

A second person told the AP the Dolphins were to host quarterback David Garrard on Monday.

Garrard, a starter for Jacksonville from 2005 to 2010, didn’t play last year. He was released five days before last year’s opener by the Jaguars, then underwent back surgery in October.

But it was Smith’s turn on Sunday

He landed at the Fort Lauderdale airport Sunday morning and arrived at the Dolphins complex at 11 a.m. EDT in a car driven by trainer Kevin O’Neill. New coach Joe Philbin, new offensive coordinator Mike Sherman and general manager Jeff Ireland arrived earlier.

Smith struggled early in his career but threw for 3,150 yards and 17 touchdowns with only five interceptions last season as San Francisco went 13-3 and made the NFC title game after an eight-year playoff drought. He orchestrated six comeback wins, four on the road.

Smith has been weighing a three-year offer from the 49ers. If he instead joins the Dolphins, he would be reunited with running back Reggie Bush. They were teammates at Helix Charter High School in La Mesa, Calif.

All were also on hand for Flynn’s 5 1/2-hour meeting Saturday.

Flynn was a backup the past four years for Green Bay, where his offensive coordinator was Joe Philbin, the Dolphins’ new head coach. Flynn has only two career NFL starts, but in last year’s regular-season finale he set franchise records with 480 yards passing and six touchdowns to help the Packers beat Detroit 45-41.

The Dolphins have started 16 quarterbacks since Dan Marino retired and are looking to make another change. While incumbent Matt Moore played well last year, there are doubts he’s a franchise quarterback. Chad Henne, who started 31 games for Miami over the past three seasons, signed Wednesday with the Jacksonville Jaguars as a backup.

The 49ers emerged as a contender for Manning when the news surfaced that he worked out Tuesday for Harbaugh at Duke. The four-time NFL MVP also worked out for the Broncos on Friday at Duke, and for the Titans on Saturday in Knoxville, Tenn.

Manning has been rehabbing in North Carolina following a string of neck surgeries, which led Indianapolis to release him.

San Francisco running back Frank Gore, who works out each offseason in Miami, said Sunday he hadn’t spoken to Smith. Gore has long supported Smith through the quarterback’s up-and-down seven NFL seasons.

Now, Gore and the 49ers are sitting tight to see what happens next.

“It’s crazy,” Gore said. “I’m waiting for whatever happens. I know coach Harbaugh and (general manager) Trent Baalke feel good about what they’re doing.”

Manning’s whirlwind free agency tour officially kicked off soon after he bid farewell to the Colts in an emotional press conference.

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AP Sports Writers Teresa M. Walker in Nashville, Tenn., Joedy McCreary in Durham, N.C., Pat Graham in Denver and Janie McCauley in San Francisco contributed to this report.

The quarterback situation for the San Francisco 49ers has generated some of the biggest news of the free agency period. From the 49ers claiming that they are not interested in signing Peyton Manning (as I discussed here) to the team now being one of three franchises in the running for the four-time MVP’s services (as I discussed here), the latest development could potentially lead the team down a very dangerous road.

After over a week of discussions, the 49ers have yet to sign incumbent Alex Smith to a contract. While a three-year offer has been in the works, talks have been stalled due to the team’s interest in Manning. Understandably, Smith has decided to take ownership of the situation by taking a red-eye flight on Saturday night to Miami to visit with the Miami Dolphins, as first reported by a Seattle Seahawks blogger on the same flight as the quarterback.

While a majority of 49er fans are either in complete favor or cautious denial of Manning’s possible migration to the West Coast, what would happen if the team misses out on the former Indianapolis Colts quarterback and Smith, who is now considering a move to the Dolphins. At first, Smith seemed to be a lock to return as the 49ers quarterback for 2012 and beyond.

Now, if this situation does not work out the right way, the 49ers could potentially be staring at Colin Kaepernick as the team’s new starting quarterback. This is something that would make backers of Manning and Smith very upset.

Even if San Francisco is the best fit for Manning in terms of personnel and his ability to win another Super Bowl, his other two likely destinations offer plenty of appeal as well. If he went to the Denver Broncos, Manning would ultimately end Tim Tebow’s reign with the team and give the team its best quarterback since the great John Elway. If he went to the Tennessee Titans, Manning would return to where it all started for him as a college quarterback with the Tennessee Volunteers and would possibly receive a lifetime contract from owner Bud Adams.

As for Smith, he has already considered changing agents because of a conflict of interests. Both he and Manning share agent Tom Condon and a change of agents would possibly expedite the process of him signing with a team. Also, a return to the Dolphins would set up a reunion of sorts with former high school teammate Reggie Bush.

Ultimately, the last thing the team needs is to start all over at a quarterback position that finally seemed to stabilize with the career year by Smith. While the saga has been intriguing to say the least, matters could blow up in the team’s face and leave the team looking at a mediocre season instead of a possible run at the Super Bowl.

Sources:

AP Source: Alex Smith visits with Dolphins Sunday, AP

The Alex Smith to Miami Story: Seahawks Blogger Breaks News, Niners Nation

Tennessee Titans work out Peyton Manning in Knoxville, ESPN

More from this contributor:

San Francisco 49ers in Running for Peyton Manning, Third Team in Race: Fan’s Reaction

Randy Moss Signing with the San Francisco 49ers is Great, but More Moves at Wide Receiver Needed: Fan’s Reaction

San Francisco 49ers not interested in Peyton Manning, have ‘offer on the table’ to Alex Smith: Fan’s Take

2011 Defensive Player of the Year Award Doesn’t Go to a San Francisco 49ers Player: Fan’s Reaction

San Francisco 49ers’ Jim Harbaugh Wins AP Coach of the Year: Fan’s Reaction

Austin Chang is a lifelong football fan, San Francisco 49ers supporter, and a Featured Contributor for the Yahoo! Contributor Network. Follow this contributor on Twitter @_austinchang.

SAN FRANCISCO – The San Francisco 49ers landed another wide receiver in a headline-making week for the NFC West champions, agreeing to terms Saturday with free agent Mario Manningham on a two-year contract.

Randy Moss joined the roster last Monday.

Now, the big question is who will be throwing them the ball: Peyton Manning or Alex Smith?

Manningham met Thursday with the 49ers, who still appear to have interest in Manning after coach Jim Harbaugh worked him out Tuesday at Duke University. Manning worked out for the Tennessee Titans on Saturday and it appears he will now choose between them, San Francisco and the Denver Broncos.

Have the 49ers done enough already to entice him, and show they’re aiming for another shot at the Super Bowl this season?

Agent Drew Rosenhaus confirmed Saturday night that Manningham, the former New York Giants wideout, had reached a deal with the 49ers, who lost in overtime of the NFC championship game to Manningham and the eventual Super Bowl champions at Candlestick Park on Jan. 22.

Manningham caught a 17-yard touchdown pass from Eli Manning with 8:34 remaining in regulation of the NFC title game to help New York reach the Super Bowl.

He had five more receptions for 73 yards in the Giants’ 21-17 Super Bowl victory over the New England Patriots, including an over-the-shoulder 38-yard catch between two defenders on which he managed to stay inbounds to start the game-winning, 88-yard touchdown drive.

The 25-year-old Manningham had 39 catches for 523 yards and four touchdowns total last year in his fourth NFL season.

Manningham will join an upgraded receiving corps that also includes Moss, who signed a one-year contract Monday, and Michael Crabtree, the team’s 10th overall pick in the 2009 draft out of Texas Tech who had 72 receptions for 874 yards and four touchdowns in 2011.

“It’s going down. Mario Manningham signs with 49ers. This is a sick WR squad. It’s going to be crazy on the Offensive side of the ball,” tweeted defensive lineman Ricky Jean Francois.

The 49ers, who ended an eight-year playoff drought in Harbaugh’s first season of 2011, also will return their entire starting defensive 11 after bringing back cornerback Carlos Rogers on a $31.3 million, four-year deal this week. So, that too could be attractive to Peyton Manning, even though there’s speculation he would prefer to stay in the AFC and not have to regularly face off with his younger brother.

Smith had been expected to re-sign with the 49ers and acknowledged he was weighing a three-year contract offer — but that all might have changed in a matter of a few days once Manning entered the 49ers’ picture. The San Francisco Chronicle reported on its Web site Saturday, citing a league source, that Smith was considering changing agents from Tom Condon, who also represents Manning.

An email to 49ers CEO Jed York, Smith and agents at CAA Sports went unreturned Saturday.