A Santa Clara County (California) grand jury has indicted Ray McDonald on one count of rape of an intoxicated person.
The District Attorney's office also charged Ahmad Brooks with misdemeanor sexual battery, the Santa Clara County District Attorney's office announced Wednesday.
McDonald was formerly with the San Francisco 49ers, while Brooks remains part of the team.
The charges stem from an incident that occurred Dec. 15, 2014, at McDonald's home. The separate assaults occurred the same evening against the same victim, according the district attorney.
"The organization is aware that a misdemeanor charge has been filed against Ahmad Brooks stemming from a December 2014 matter," 49ers general manager Trent Baalke said in a statement. "We take any charge against a member of this organization seriously and are in communication with the NFL. Ahmad is returning home to California and will not participate in Saturday's game."