Toomer's Corner is where Auburn fans gather and cover the two trees with toilet paper to mark sports victories and other celebrations.
Early Thursday morning, Auburn police arrested Harvey A. Updyke Jr., 62, on a charge of first-degree criminal mischief. The charge is punishable by one to 10 years in prison and up to $15,000 in fines. He was being held on $50,000 bond.
Updyke is suspected of using a powerful herbicide, Spike 80DF, to poison the historic trees.
Spike 80DF, or tebuthiuron, can remain in the soil for three to five years and can inhibit growth for up to seven years, said Gary Keever, an Auburn horticulture professor.
The trees aren't likely to survive, Keever said.
Updyke, meanwhile, could face more charges, Auburn police said.
The use of a herbicide for purposes other than what is stated on the label is a federal crime.
A man identifying himself as "Al from Dadeville" called Paul Finebaum's nationally syndicated radio show last month and said that he had poisoned the two trees. The caller signed off by saying, "Roll damn Tide."
Throughout the afternoon at Toomer's Corner, people were leaving flowers, orange and blue shakers, notes, teddy bears and other items at the base of each of the trees.
Auburn seniors Sarah Willis, of Silver Hill, Ala., and Elizabeth Cammon, of St. Louis, wrote messages on rolls of toilet paper such as "get well soon" and "War Eagle," Auburn's traditional battle cry.
They placed the rolls at the bottom of the one of the trees, took photos and hugged it.
"I've never been a tree-hugger before, but I am now," Willis said.