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Knowledge of the Thelodonti has improved greatly in recent years, but phylogenetic relationships remain poorly understood. We revised the data from an earlier phylogenetic study and added 15 scale-based species. Maximum parsimony analysis gives a well-resolved tree in which Archipelepis and Boothialepis form a basal clade, recognized here as the order Archipelepidiformes, sister group to two large clades also recognized as orders. The first is recognized as the order Furcacaudiformes, including Nikolivia, Lanarkia, Phillipsilepis, Pezopallichthys, Drepanolepis (in the new family Drepanolepididae), Barlowodus, Apalolepis, and Furcacaudidae. The second, here recognized as the Thelodontiformes, contains Turinia, Thelodus, Stroinolepis, Loganellia, Longodus, Helenolepis, Phlebolepis, Erepsilepis, Trimerolepis, Eestilepis, Valiukia, Paralogania, and Shielia.

Thelodont phylogeny revisited, with inclusion of key scale-based taxa