The robbery happened around 1 p.m. on Friday at San Bruno Liquors on San Mateo Avenue, police said.
Police have not disclosed how much money was taken at gunpoint, but they did say the suspect fled in a black four-door sedan.
Later Friday evening, police officials said they found evidence allegedly linking a South San Francisco resident to the crime.
Police officials have named 30-year South San Francisco resident Luis Magana as the suspect.
Authorities are still investigating this case, and ask that anyone with additional information contact the Police Department at (650) 616-7100.