Flores (shoulder) was optioned to Triple-A New Orleans on Sunday, MLB.com's Joe Frisaro reports.
Flores was called up to serve as the Marlins' 26th man during Saturday's doubleheader with the Nationals, but had to leave his start in Game 2 after three innings due to a right shoulder strain. That injury ended up landing the right-hander on the disabled list, but since he was just a temporary player, he will be placed on the minor league DL. Once ready for activation, Flores will play at the Triple-A level, where he owns a 2.59 ERA on the season.