It was first described in 1885 by Hermann Burmeister, who described the genus based on two upper and two lower molars found near the mouth of the Chubut River in Argentina.

In the early 1900s, Florentino Ameghino described other species of Colpodon, C. distinctus and C. plicatus, and believed that this animal was a member of the family Leontiniidae.

[2] Moreover, other fossil remains assigned to this genus have been found in the Chichinales Formation of Río Negro Province in Argentina.

[3][4] Colpodon is currently considered a derived member of the family Leontiniidae, a group of heavy-built notoungulates common during the Oligocene.

The 2012 study showed a close relationship between Colpodon, Huilatherium and Taubatherium, two leontiniids from a tropical clade whose remains have been found in Colombia and Brazil.