Derick Almena and Max Harris are facing multiple counts of involuntary manslaughter.
Mr Almena was leaseholder at the warehouse, a bohemian collective and living space for about 20 people, and Mr Harris was his deputy.
The 2 December 2016 fire broke out during an illegal rave at the venue, known as the Ghost Ship.
Investigators have not determined the exact cause of the blaze, which was the deadliest in the US for more than 10 years, though local media reports have cited a faulty electrical system as a possible cause.
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All the victims - who ranged in age from 17 to 61 - died of smoke inhalation as they struggled to flee down a makeshift staircase made from wooden pallets, investigators say.
Alameda County District Attorney Nancy O'Malley announced criminal charges at a press conference on Monday.
"Defendants Almena and Harris knowingly created a fire trap with inadequate means of escape," she said.
"They then filled that area with human beings and are now facing the consequences of their actions."
"They acting knowingly and disregarded the risk" by allowing people to live in the building and by lying to police about how the space was being used, Mrs O'Malley added.
Mr Almena held the lease for the Ghost Ship, collected rent from sub-tenants and decided who could live or work at the collective.
Harris, who considered himself "creative director", helped collect rent while mediating disputes among tenants and with the building's owners, say prosecutors.
If convicted the two face up to 39 years in prison.
Mr Almena found himself the target of widespread criticism for a social media post after the tragedy when he lamented that "everything I worked so hard for is gone".
The father-of-three had added that his family was safe without mentioning the three dozen deaths.
Two people have been arrested over a warehouse fire last year in Oakland, California, that left 36 people dead.