Flores, 22, played last season at Class A St. Lucie in the Florida State League, batting .266 with 21 home runs and 70 RBIs in 120 games. The year was a rebound campaign for Flores, who broke his right thumb in an exhibition game at RFK Stadium before the 2005 season.
Selected from the Mets' Triple-A roster for $50,000, the Nationals must keep Flores on their 25-man Major League roster for the 2007 season or offer him back to the Mets for $25,000.
"We're disappointed, because we like Jesus a lot, but we'll see how the process plays out," said Mets director of Minor League operations Adam Wogan. "We still feel like we have some young catching prospects, between Drew Butera, Francisco Pena and Sean McCraw."
Of that trio, Pena -- a 16-year-old international signee -- likely has the highest ceiling, though all three are still ticketed for the low Minor Leagues. Mets general manager Omar Minaya has planned a Dominican Republic scouting trip for this week centered around seeing Pena, the son of Yankees coach Tony Pena.
Butera, 23, is regarded as an excellent defender but batted just .186 in 95 games for Class A Hagerstown last year. McCraw, 20, split his year between Rookie-league Kingsport and Class-A Brooklyn.
In the Minor League phase of the Draft, the Mets selected left-handed starter Ricardo Morales from the Nationals' Double-A roster.
Morales, who turns 23 on Saturday, was 6-10 with a 4.70 ERA in 25 games (23 starts) for Class A Potomac of the Carolina League. In 132 innings, Morales walked 42 and struck out 69. He also made one start, a win, at Double-A Harrisburg.
"He's a good young lefty who is healthy, projectable and has good command," Wogan said. "That's probably what we like the most. We figured it was worth taking a shot for $4,000."
The Mets also lost a pitcher, right-hander Moises Robles, in the Minor League phase. Robles was selected by the Pirates from the Mets' Double-A roster and had pitched well in the Dominican Summer League, going 1-2 with a 0.60 ERA and six saves in 19 games.
"You're never happy with losing anybody," Wogan said. "I think for Robles, it's good for him to get an opportunity. We didn't know if we were going to have a chance to know him all that well in the States."
Bryan Hoch is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.