It happened before 11 pm Tuesday in the parking lot of the Economy Inn on Blackstone and Swift Avenues.
The victim, a man in his early 20s, was shot in the upper body. He was taken to a hospital for treatment and is expected to recover.
The victim was staying at the motel.
"This does appear to be gang motivated. This was not a random shooting. This was an intended target," said Fresno Police Lt. Ignacio Ruiz.
Investigators said two people were seen leaving the area after the shooting. A description of possible suspects or the vehicle was immediately available.
Anyone with information is asked to call the Fresno Police Department.