The body was found around 7:30 a.m. in a small parking lot near Fourth Street and Tamalpais Avenue by a business owner arriving for work, police spokeswoman Margo Rohrbacher said.
The lot is at the eastern end of the downtown area and there are several bars, a pizza restaurant, a liquor store and a bus terminal nearby.
Police have tentatively identified the woman, who is between 25 and 35 years old, but are not releasing her name until the identity is verified and her family is notified.
Police said the official cause and manner of death have not been determined and an autopsy is scheduled for Wednesday.
Anyone with information regarding the case or who may have witnessed suspicious activity in the area Monday night is asked to call San Rafael police at (415) 485-3000 or Crime Stoppers at (415) 472-2746.
