The blaze broke out during an electronic dance party, killing those who could not escape from the dilapidated two-story warehouse. One of two exits to get away from the fire had been blocked, authorities said.
O'Malley told reporters on Monday that the two men "knowingly created a fire trap with inadequate means of escape. They then filled that area with human beings and are now facing the consequences of their action."
Almena and Harris face up to 39 years in prison if convicted of all charges. They were arrested earlier in the day.
Assistant District Attorney Teresa Drenick did not provide information about Harris, but a probable cause document said he lived at the warehouse and was a creative director, collecting rent and acting as an intermediary between Almena and warehouse owners.
Almena at the time apologized to the victims' families and vehemently defended himself, saying he would never have intentionally endangered any of his tenants.
"I'm only here to say one thing: that I am incredibly sorry," he told NBC's "Today."
Almena's attorneys on Monday said: "We intend to vigorously defend him in the court of law. We believe that these charges represent no less than a miscarriage of justice, and we are confident that this attempt to make a scapegoat out of our client will fail."
CNN was attempting to reach an attorney for Harris.
O'Malley said the men were reckless, creating a risk of death. She said, among other things, they allowed up to 25 people to live in the warehouse and deceived officials and the building owners about that fact. Almena and Harris allowed the floor-to-ceiling storage of large quantities of flammable materials, she said.
"We continue to mourn the loss of the 36 young vibrant men and women ... who should be with us today," the prosecutor said.
Complaints were filed weeks before fire
Darin Ranelletti, Oakland's interim director of planning and building, told CNN last year the warehouse had not been inspected in 30 years.
"That means we had no applications for permits in the last 30 years, and there were no violations that were submitted for interior work within the main building attributed to that street address," he said.
The most recent complaints were filed three weeks before the fire.
Inspectors went to the property in November to investigate a complaint about blight and an illegal structure in the lot next door, Ranelletti said. The lot has a different address than the warehouse.
Ghost Ship, along with an adjacent lot, had become cluttered with old cars, oil containers, pests and trash, according to complaints.
Many of the complaints were directed at the lot, pointing to a "ton of garbage piling up on the property" as well as the "illegal interior building structure" at the warehouse, according to city records
The probable cause document said Almena "allowed and encouraged tenants to use nonconventional building materials that he collected to create their living spaces. These nonconventional building materials included recycled dry wood, such as fence boards, shingles, window frames, wooden sculptures, tapestries, pianos, organs, wooden furniture, RV trailers, rugs, and other ramshackle pieces."
Officials said the exact cause of the fire may remain undetermined because of the severe damage to the building's contents.
Lawsuits claim dangers were known
Following the fire, the families of victims Griffin Madden and Michela Gregory filed lawsuits against the building owner and employees of various city and county departments. The families claimed they knew the warehouse posed dangers long before the deadly blaze.
Among those who should have been aware of the hazards are members of the Oakland Fire Department who "attended and held a music event" there prior to the deadly fire, the lawsuits say without elaborating. The lawsuits note that the nearest fire station is about a block away.
In addition to claims against Oakland and Alameda County, the Maddens and Gregorys targeted building owner Chor Nar Siu Ng and landlords Micah Allison and Almena.
The lawsuits also name as defendants a promoter, a California-based music label, a Madison, Wisconsin-based musician and two landlords of nearby properties who "provided utilities and services to the Ghost Ship, including a supply of electricity from their premises and a restroom on their premises for use by patrons and invitees during music and other events."
Drenick would not say whether more criminal charges will be filed. "As of today, the charges that we filed are the charges that stand." She said the office has completed its investigation.