DA Nancy O'Malley says they could get up to 39 years in prison for these charges.
The criminal complaint filed alleges the Almena created a "dangerous condition" and "firetrap" that cost 36 people their lives.
PHOTOS: A look inside the Oakland Ghost Ship collective warehouse
Ghost Ship founder Derick Almena was arrested in Lake County this morning, while Max Harris was arrested in Los Angeles County.
Thirty-six people died in the fire in December, making it the nation's deadliest structure fire in more than a decade.
Nearly all of the people who died in the blaze at the warehouse at 1315 31st Ave. on Dec. 2 were attending a dance party on its second floor.
MORE: Ghost Ship fire causes safety concerns for LA-area co-ops
A recent lawsuit that was filed on behalf of the families of half of the 36 victims alleged that the warehouse was "a death trap that contained a maze of makeshift rooms, alcoves and partitions" and lacked a safe means of getting out.
Source: 2 arrested for Ghost Ship fire that killed 36 people
Several weeks after the fire, Almena's attorney said he didn't engage in any criminal misconduct and alleged that governmental agencies were responsible for the blaze for not cracking down on code violations at the warehouse.
Bay City News contributed to this report.