Smith left the Miami complex after a 5 1/2-hour meeting. Dolphins officials declined to comment on any details about this visit.
Smith and Manning have the same agent, Tom Condon.
A new starting quarterback would be the Dolphins' 17th since Dan Marino retired following the 1999 season. Winless in postseason since 2000, they made signing Manning their top offseason priority, but he told them Thursday he would sign elsewhere.
The Dolphins planned another QB interview Monday, when they were to host veteran David Garrard, a person familiar with the negotiations said. The person confirmed the visit to The Associated Press on condition of anonymity because the team had not publicly discussed its plans.
Garrard, a starter for Jacksonville from 2005 to 2010, didn't play last season. He was released five days before the opener by the Jaguars, then underwent back surgery in October.
"Looks like Miami (is) going with Moore again," former Dolphins coach Jimmy Johnson tweeted after Flynn's deal with Seattle was announced.
While Moore played well last year, there are doubts he's a franchise quarterback.
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.