KCBS reporter Holly Quan at the scene says investigators expect to be at the fire scene all day attempting to figure out what caused the blaze in the converted Victorian structure.
Three flats were built into the structure on Hyde between Jackson and Washington.
Firefighters were called to the building around 3 a.m. to find one panicked woman on the second floor about to jump from a burning window. Firefighters ran an escape ladder to her and managed to get her to safety.
Initially one person was killed; three others including two firefighters were hospitalized for minor injuries.
Fire Department spokesman Pete Howes says that during mop up, firefighters discovered a second body. "The smoke is banked all the way down to the floor. These firefighters are trying to do the search, crawling on their hands and knees while their brothers and sisters are fighting the fire at the same time. It's not unusual for people to gravitate towards debris or some apartments have more materials in them than others and so the firefighters went through them and did find one more person," he said.
At least thirteen people were evacuated from surrounding buildings.
The Red Cross is attempting to find them housing.