The suspect is identified as 27-year-old John Flores.
Investigators say he was arrested on Thursday after serving a search warrant at a home off Highway 59 and Mission Avenue.
Flores is accused in the September 9 homicide of a 15-year-old boy, identified by his family as Mario Fertini.
That shooting happened on Bear Creek Drive near Brookside Drive.
Investigators say Flores is a known gang member.
He is booked into the Merced County Jail with a bond set at $1 million.
Merced Police are now asking for the public's help in identifying the second suspect in this case.