Smith, a longtime San Francisco 49ers quarterback, arrived at the Dolphins' complex in a car driven by trainer Kevin O'Neill and later left after a 5½-hour meeting. Coach Joe Philbin, offensive coordinator Mike Sherman and general manager Jeff Ireland arrived at the complex before Smith and O'Neill did.
The 49ers had been working to re-sign Smith, reportedly offering him a three-year, $24 million contract, but they also went to North Carolina last Tuesday to watch Manning work out at Duke University.
Smith and Manning have the same agent, Tom Condon. However, Smith reportedly might sever ties with Condon.
A new starting quarterback would be the Dolphins' 17th since Dan Marino retired following the 1999 season. But after all of their shopping, it's possible Miami will stick with incumbent Matt Moore, who played well last season (2,497 passing yards and 16 touchdowns with nine interceptions), although there are doubts he's a franchise quarterback.
Flynn has ties to Philbin, who was the quarterback's offensive coordinator with the Green Bay Packers.
The Dolphins also have scheduled a meeting with free-agent quarterback David Garrard, a league source told NFL Network insider Jason La Canfora.
The Associated Press contributed to this report.