The investigation had been at a standstill for months until a tip lead police to Riley.
On Monday, Riley was escorted into the Spencer County courthouse for his initial hearing where he faces two counts.
"Count one is murder, count two is obstruction of justice," said Spencer County Prosecutor Kelly Corne.
The first count is for the murder of Cain on or before May 2012.
Detectives say Cain's body was found in a rundown barn off of State Road 66 between Grandview and Troy. Investigators believe Cain's body was found weeks after he was killed.
The count of obstruction of justice stems from investigators' claim that Riley altered the crime scene.
Although charges have been filed, Spencer County Coroner Robert Fuller says they are still waiting on DNA results to positively identify the body.
"At this point, the charges state for the murder of Brian Cain. The victim is believed to be Brian Cain, that is what the probable cause affidavit states," Corne states. "There will be a formal investigation, but the victim is believed to be Brian Cain."
A progress hearing was set for September 28 and Riley was also appointed an attorney by the court.
Riley could face 45 to 65 years for murder and up to three years in prison for obstruction of justice.
Riley is being held without bond.
At that progress hearing, we will find out if there is a resolution or if Riley will go to trial for murder.
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