The fire marshal says the boys intentionally set fire to the gymnasium of Mesa Verde Elementary school earlier this month.
The fire was contained to the gym but, the damage is extensive.
The 11 and 13 year old boys allegedly had been playing basketball in the gymnasium earlier in the day but, somehow managed to get back in, or stayed behind after hours.
The fire marshal says there was no sign of forced entry. Meaning the doors may have been left unlocked.
The fire originated in a closet of the gym and spread to the area where the teacher's office is located.
While the fire was contained in those areas, there is heavy smoke and water damage.
Deputy fire marshal Jacob Diaz says they quickly realized the fire was set intentionally.
"On the night of the fire we had a couple of witnesses that identified two possible juveniles that had been in the gymnasium just prior to the fire being discovered. So we were able to identify, track em down and then eventually talk to them." Diaz said.
The boys were arrested Thursday night and are being held in the Youth Center of the High Plains.
They're expected to stay there at least through the weekend.
Diaz won't say exactly how they started the fire citing the ongoing investigation.
Damage was originally estimated to be as much as $250,000.
Investigators say a revised estimate puts that number as high as $400,000.
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