Muno, the Mets' No. 1-ranked Minor League shortstop, received a 50-game suspension after testing positive for a metabolite of Drostanolone, an anabolic steroid sometimes used by bodybuilders.
Rojas tested positive for Stanozolol, a synthetic anabolic steroid commonly sold under the name Winstrol.
Both suspensions are effective immediately.
Muno, a 23-year-old out of Fresno State, is hitting .283 with five homers and 23 RBIs for Class A Advanced St. Lucie in the Florida State League. The switch-hitter was New York's eighth-round pick in last year's Draft and earned MiLB.com Organization All-Star status after hitting .355 with two homers, 24 RBIs and nine steals as a New York-Penn League All-Star with Class A Short-Season Brooklyn.
Muno is the third St. Lucie Met to receive a ban this season following Dock Doyle and Scott Moviel, who were suspended for drugs of abuse on Feb. 9.
Rojas, a right-handed reliever originally signed by the Mets in 2006, owns a 3.38 ERA with nine strikeouts in eight innings for Class A Advanced San Jose in the California League. He spent the previous five seasons with the Mets at the Class A level.
Major League Baseball has now suspended 42 players this year for violations of the Minor League Drug Prevention and Treatment Program.