Police said the robbery happened around 3:42 a.m., Saturday, at the Wakulla Motel at 3550 North Atlantic Ave.
A man came into the motel and showed a handgun to the desk clerk while demanding cash, officers said.
Police said the man left the hotel on foot.
The robber was described as a man approximately 20 to 30 years old. He was seen wearing a gray baseball cap, black shirt, jeans and black shoes. Police said the man has a tattoo down his left arm from the elbow to the wrist.
Police are asking anyone who may have seen the man to call Crimeline at 1-800-423-TIPS.