The women were located separately within the small city of Weed, which is about 225 miles north of Sacramento, it said.
"The Siskiyou County Sheriff's Office would like to extend its condolences to the friends and family of the deceased," it said. "Please join us in keeping the community in your prayers during this time.
No further information about the victims was released.
The women died in Mill Fire, which erupted Friday in Siskiyou County and has spread to 4,254 acres with 40% contained, the California Department of Forestry and Fire protection said in a Sunday night update.
In addition to the two deaths, three civilians have been injured as well as 50 structures destroyed and another three damaged.
The fire is currently threatening another 411 structures, it said.
A fire fighter stands watch over a destroyed neighborhood, after the Mill Fire burned through parts of Weed, Calif., on Saturday. Photo by Peter DaSilva/UPI
The Siskiyou County Sheriff's Office has issued several evacuation orders over the weekend, some of which have since been lifted, allowing some people to return to their homes. In the late Sunday update, Cal Fire said 559 people have been evacuated.
Cal Fire said firefighters "held and improved containment" of the fire over Sunday and that "the fire is not anticipated to spread."
The fire erupted as a California braced for extreme weather over the holiday weekend.
Siskiyou County firefighters were also responding to Mountain Fire, which erupted Friday, and has grown to nearly 8,9000 acres, with 10% contained, though there have been zero civilian casualties reported.
Some 330 people were under evacuation orders due to the blaze as it burns in a steep, broken terrain covered by various types of vegetation.
The cause of both fires are under investigation.