The incident was reported at about 4:30 p.m. at the bookstore at 313 Corte Madera Ave., according to police.
The girl was near some book displays when a man approached her and made her touch his genital area, police said.
The suspect then quickly left the store, and although the girl immediately told her mother, the suspect could not be found by the mother or store employees, who then called the police.
The girl did not sustain any injuries in the incident, according to police.
The suspect is described as a Hispanic man between the ages of 18-25 years old. He is about 5 feet 6 inches tall with short black hair and was clean shaven, police said.
He was wearing a white T-shirt with a black jacket and black pants and white tennis shoes during the incident.
There was a previous incident where a man molested an 8-year-old girl at the same bookstore on June 14, according to police.