The Aggies zeroed in on Hooten earlier in the week, sources said, and were able to close the deal despite Sam Houston's attempts to keep him from its intraconference rival.
"I believe Coach Hooten is a tremendous fit for New Mexico State," athletic director Mario Moccia said. "Throughout his coaching career, he has demonstrated an ability to build hard-nosed, defensive-minded teams. Importantly, his programs are always modeled on character and integrity."
Hooten joins the Aggies after 13 seasons at Sam Houston, where he racked up six 20-win seasons and at least 18 wins in each of the last 10 seasons. He guided the Bearkats to the Southland regular-season championship in 2019 and also landed the top seed in this season's WAC tournament.
Prior to becoming Sam Houston's head coach, Hooten was an assistant coach with the Bearkats for six seasons.
With Hooten's hire, New Mexico State is hoping to turn the page from an ugly season that left a cloud over the Aggies' program. They canceled their season in February after hazing accusations against three players. A police report cited three players for false imprisonment, harassment and counts of criminal sexual contact against a teammate.
Three months earlier, a New Mexico State player, Mike Peake, shot and killed a New Mexico student in what police have called self-defense. Multiple investigations have been launched to determine whether coaches and staff members cooperated with police and were forthcoming with evidence following the shooting.
Hooten replaces Greg Heiar, who was fired shortly after the season's cancellation in February.