Jonathon Cooper is behind bars in a Colorado jail ... after the standout Broncos linebacker was arrested Thursday night around 11 PM, TMZ Sports has learned.

It's unclear what led up to the arrest, but the 6th-year pro is being held on two counts of domestic violence, as well as criminal mischief.

The 28-year-old was booked into a detention facility at 2:38 AM.

JC is scheduled to go before a judge this morning ... and he's got another hearing set for Monday.

Cooper was a seventh-round draft pick out of Ohio State in 2021, and he's been a steal.

Last year, Jonathon was a major part of the Broncos' dominant defense. He racked up 8 sacks and 50 combined tackles in 17 games.

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