It happened just before 2:00 am at the Renaissance Apartments on Blackstone and Illinois Avenues.
Investigators say the victim and another man got into an argument. The suspect fired two shots from his shotgun, hitting the victim's legs.
The suspect ran through an alley to escape.
"We had an active search scene for the suspect, but he was not located. (The) firearm still outstanding, so we ask if anybody saw the individual or know where he's at, please use caution and contact the police department," said Fresno Police Lt. Israel Reyes.
Police say the victim is in his 60s. He was taken to Community Regional Medical Center, where he's expected to recover.
Investigators do not believe the shooting was gang-related. Officers were working on getting surveillance video to review for the investigation.