Nicholas D'Agostino, 20, was arraigned Friday afternoon in Riverhead. Police say he killed Yusef Staine.
Police believe D'Agostino and Stain knew each other and were traveling together.
Suffolk County District Attorney Ray Tierney said the two men were friends and that D'Agostino came from Arizona to visit Staine before killing him.
There is no word on what the motive was, but prosecutors say the suspect shot the victim in the back of the head and then again in the torso when he collapsed.
Prosecutors say D'Agostino left the scene and eventually boarded a Greyhound bus to Arizona nearly 24 hours after the killing.
"He was wearing a mask, and he though no one could see him, but our law enforcement partners are always watching and through their hard work we were able to unmask this defendant and hold him responsible," Tierney says.
D'Agostino was charged with second-degree murder.
"He absolutely maintains his innocence," says D'Agostino's attorney, George Duncan. "He had nothing to do with this crime."
If convicted, D'Agostino faces 25 years to life on the murder charge and a possible 40 years to life if that runs consecutive with the pair of weapons charges.
He was held without bail and is due back in court on June 14.