The inclusion of Utaherpeton in various phylogenetic analyses has resulted in multiple phylogenies (hypotheses of evolutionary relationships) that are very different from one another, making it a significant taxon in terms of understanding the interrelationships of lepospondyls.

A unique anatomical feature that distinguishes Utaherpeton from other "microsaur" lepospondyls is a connection between the prefrontal and premaxilla bones at the front of the skull.

[1] When Utaherpeton was first described in 1991, it was tentatively classified within a group of "microsaurs" called Microbrachomorpha, which included the better-known Microbrachis.

[1] A 2001 phylogenetic analysis found Utaherpeton to be the most basal lepospondyl, followed by the "microsaur" Hyloplesion, which has also been considered a microbrachomorph.

However, Microbrachomorpha was not recognized as a true clade because Microbrachis was found to be more deeply nested within Lepospondyli, more closely related to derived lepospondyls like nectrideans and aïstopods than to other "microsaurs".