The Pride crosswalk at the intersection of Church and Columbia streets had just been unveiled on Monday morning.
Police say several witnesses saw a 91-year-old man pouring white paint over the crosswalk after 8 p.m. PT.
"This happened early in the evening when a lot of people were around, so a whole bunch of people were calling 911," said Insp. Todd Matsumoto.
Matsumoto said police found the elderly man a few blocks away. He was arrested and taken to a nearby hospital for evaluation.
The police investigation is ongoing. Matsumoto said the man will likely face a charge of mischief and if this qualifies as a hate crime will be evaluated during the investigation.