Santana was scratched Monday from his next scheduled start because of discomfort in his pitching elbow. Francoeur has a torn ligament in his left thumb, leaving New York without its right fielder and top hitter.
The setback involving Santana is particularly alarming for the fourth-place Mets, who are counting on the two-time Cy Young Award winner to lead their rotation for years to come.
"He has not been throwing between starts for quite awhile. I would say since before the All-Star break. He has been pitching with this problem, but not with the level of discomfort he has now," New York manager Jerry Manuel said Monday after his team's 6-2 loss to Philadelphia.
"I'm terribly concerned," Manuel told Newsday. "No question about it."
Francoeur told MLB.com that he spoke with Santana about the likelihood of surgery. He told the Web site Santana "can get it looked at now and be two months ahead by Spring Training," indicating a need for surgery in the immediate future.
Mike Pelfrey, Santana's fellow starter, added, "I don't think anyone expects good news."
Santana had been slated to pitch Tuesday night in Florida. Instead, the left-hander will be examined by Mets medical director Dr. David Altchek and undergo an MRI, according to multiple media reports.
"I hope to have some definitive word for you tomorrow," Manuel said.
Right-hander Nelson Figueroa will start against the Marlins.
Santana is 13-9 with a 3.13 ERA in 25 starts during his second season with the Mets. He was acquired in a February 2008 trade with Minnesota.
Santana was unavailable for comment after Monday's game. New York catcher Brian Schneider said the pitcher's stuff hasn't been up to par lately.
"What I'm looking at is his location, which, like I said, hasn't been as sharp as it had been," Schneider said.
New York also learned Monday that Francoeur has a torn ligament in the thumb on his non-throwing hand. He is day to day, the club said, but is expected to miss at least a handful of games.
"The right thing now is to let the swelling go down. It's kind of big," Francoeur said. "I'm going to try to play through it to the end of the season. If I can rest it for two or three days and then play, I'm going to do it. You might say, 'Why bother? We only have 38 games left.' But I came here to play and I want to play."
Acquired last month in a trade with Atlanta, Francoeur was injured Sunday while making a diving catch. X-rays were negative, but his thumb swelled up afterward and he went to the hospital Monday for an MRI, which revealed the tear.
Since joining the Mets on July 11, Francoeur has been the team's most productive hitter. He is batting .305 with six homers and 24 RBIs in 39 games. He also has eight doubles and two triples.
"Hopefully, the swelling goes down quick and I can get back in there. I've been fortunate that in four or 4 1/2 years I have never missed a game because of injury," Francoeur said.
Francoeur lined into an unassisted triple play by Phillies second baseman Eric Bruntlett on Sunday, ending New York's 9-7 loss. It was the second time in major league history a game ended on an unassisted triple play -- Detroit first baseman Johnny Neun also turned the trick in 1927.
In other news, Wright took grounders on the field before the game and said he still expects to come off the disabled list Sept. 1 in Colorado.
The All-Star third baseman has been sidelined with a concussion since getting hit in the head with a fastball from San Francisco pitcher Matt Cain on Aug. 15.
"I'm really itching to get back out there," said Wright, who has been taking batting practice indoors.
Wright said he isn't experiencing any post-concussion symptoms and he hopes to take BP on the field Tuesday -- but he won't travel with the Mets during the first part of their upcoming road trip.
New York plays three games in Florida beginning Tuesday, then three at the Chicago Cubs before opening a series at Coors Field on Sept. 1.
"It felt good to go out there and finally put the spikes back on," Wright said. "Still on schedule. Still on track."
The Mets also recalled left-hander Ken Takahashi from Triple-A Buffalo and optioned lefty Pat Misch to their top farm club.
Takahashi, a 40-year-old rookie from Japan, was 0-1 with a 3.00 ERA in 15 relief appearances for the Mets earlier this season. He relieved starter Bobby Parnell in the sixth inning Monday and tossed 1 1/3 scoreless innings.
Information from The Associated Press contributed to this report.