Ramiro Gutierrez, 26, was also charged with gang assault and criminal possession of a weapon.
Police said he is a member of the MS-13 gang and has been arrested before.
“We have had a number of incidents involving MS-13 in recent months,” said NYPD Chief of Detectives Dermot Shea. “They are suspected in a number of troubling incidents in Queens in the last year or two.”
Watch: NYPD On Subway Platform Shooting Investigation
Around 1 p.m. Sunday, an argument aboard the 7 train spilled onto the platform at the 90th Street-Elmhurst Avenue station in Jackson Heights.
Police said Gutierrez pulled a gun and shot the victim, identified as 20-year-old Abel Mosso, multiple times in the face.
Mosso was a member of another gang, police said.
“It’s definitely gang related,” Shea said.
Police are searching for two people wanted for questioning in the case. They’re described as Hispanic men, 30 to 35 years old. One was last seen wearing a dark color hat, red scarf, dark sweatshirt, dark pants and white sneakers. Another, who has a slim build, was seen wearing a gray hooded sweatshirt, black pants and black sneakers.
Anyone with information is asked to call NYPD’s Crime Stoppers hotline at 1-800-577-TIPS (8477) or 1-888-57-PISTA (74782) for Spanish. You can also submit a tip via the Crime Stoppers website, by Tweeting @NYPDTips or by texting a tip to 274637 (CRIMES) and then entering TIP577.