Debra Schmitt, 53, was found dead in a creek bed near her home in Ross at about 9:50 a.m., police said.
Earlier reports said Schmitt had been found in the afternoon, possibly in the backyard of her home, according to a police officer who didn't want to be named.
Schmitt was considered missing after she failed to show up to class Thursday morning at Terra Linda High School at 320 Nova Albion Way in San Rafael.
The words "thank you everyone" were written on a blackboard in Schmitt's classroom, and Schmitt's keys to the school were found in the classroom, San Rafael police spokeswoman Margo Rohrbacher said.
Ross police initially searched trails in the Phoenix Lake area because Schmitt liked hiking.
Schmitt may have been in need of prescription medication, Ross police Sgt. Gianfranco Campa said.
Schmitt was married with a son, and she left her Toyota, purse and identification papers at her home, Campa said.
Police are aware some of Schmitt's relatives in New Jersey have died within the past year and that Schmitt's husband filed for divorce, but Campa said police don't believe that is why she went missing.
An initial examination of Schmitt's body did not reveal signs of foul play. The results of the full investigation will not be available for several weeks, according to the Ross Police Department.