An outside investigator found nine alleged rapes or sexual assaults involving students had occurred between September 2010 and December 2011, including at least two that hadn't been reported.
In one case, former Montana football player Beau Donaldson pleaded guilty to rape and was sentenced to 10 years in prison.
The situation has left some worried that the football program while successful on the field was out of control off it.
The rape accusation against Johnson has created a buzz across Missoula, a town that centers on the university, and a state where UM football is the top sports attraction.
Only two people among the first 39 seated in the jury box raised their hands when Assistant Attorney General Joel Thompson asked who hadn't heard about the case against Johnson.
"Does anybody feel like they're just too big a Griz fan to be on this case?" Thompson then asked.
Nobody raised a hand.
Johnson is accused of raping an acquaintance while they watched a movie at her residence last year. Johnson says the sex was consensual.
On the eve of the trial, former U.S. Rep. Pat Williams, who is now on the board that oversees Montana's university system, said UM is recruiting "thugs" for its football team.
The Democrat made his comments in a Thursday New York Times story, then repeated them in an interview with Missoula radio station KGVO-AM. He said there have been too many UM athletes convicted or suspended over rapes, assaults or burglaries during the past year.
Williams said he was not speaking about Johnson.
"We need a better recruiting system because the current recruiting system is letting in too many thugs. And that has to stop," Williams told the station. "As a member of the Board of Regents, I intend to do what I can to make sure that this very limited thuggery stops."
The Board of Regents distanced itself from the comments, saying Williams was speaking for himself.
"We as a board do not agree with the statements made," Board of Regents Chairwoman Angela McLean said in a statement.
A prosecutor's affidavit said Johnson and the alleged victim had known each other since 2010 and decided to watch a movie at her house on Feb. 4, 2012.
The woman told investigators Johnson held her down and forced her to have sex with him in her room despite her protests.
Court records show the woman texted her roommate: "Omg ... I think I might have just gotten raped ....he kept pushing and pushing and I said no but he wouldn't listen ... I just wanna cry ... Omg what do I do!"
Johnson, in a motion to dismiss the case, said the woman had flirted with him the night before at a party and consented to sex the next night, even asking if he had a condom.
The motion also claimed the case was filed by county prosecutors to send a message about their efforts to pursue rape cases.
Last April, the federal Department of Education announced it was investigating a complaint alleging the university discriminated against female students, faculty and staff by failing to address a sexually hostile environmental caused by its failure to appropriately respond to reports of sexual assault.
Soon after, the U.S. Justice Department announced its investigation into the handling of rape investigations and prosecutions, and the school announced in May the NCAA had been investigating its athletic programs for undisclosed reasons.
The Department of Education said this week it had closed the discrimination complaint because the allegations were being addressed by the Department of Justice investigation. The Justice Department and NCAA investigations continue.
Johnson's case surfaced on March 9, when the female student obtained a temporary restraining order against him. He was briefly suspended from the football team then reinstated when a civil no-contact order replaced the restraining order.
Coach Robin Pflugrad enthusiastically welcomed him back to spring drills and lauded his "character and tremendous moral fiber."
The woman's lawyer, Josh Van de Wetering, quickly complained to the athletic department that the comment left his client "less than confident in the university's commitment to protect her."
Three days after coach Pflugrad welcomed Johnson back, university president Royce Engstrom announced he was not renewing the contracts of the coach and athletic director Jim O'Day. Both were immediately relieved of their duties, without an explanation from Engstrom.