Harvey Almorn Updyke has been charged with allegedly applying toxic doses of a tree-killing herbicide to the live oaks at a place called Toomer's Corner. Auburn students traditional drape the trees with toilet paper after a football victory and did so again this week to honor the trees.
Auburn officials said they will do what they can to save the trees, but the school's athletic director said it would take "divine intervention" to do so.
Updyke admitted calling a sports radio talk show about the poisoning of the trees, but denied actually doing it.
The 62-year-old former Texas state trooper, who did not attend Alabama but named his sons Crimson and Bear, was jailed on a charge of criminal mischief.
The traditional Alabama-Auburn football rivalry was particularly charged this year because not only did Auburn go on to win the national championship, there was a dispute about the eligibility of its quarterback, Cam Newton.