Pygopodoidea is a gecko superfamily and the only taxon in the gekkotan subclade Pygopodomorpha. The clade includes three Australasian families: Diplodactylidae (stone geckos), Carphodactylidae (knob-tailed geckos), and Pygopodidae (flap-footed geckos). Traditional gekkotan systematics had considered Diplodactylidae and Carphodactylidae as subfamilies of the family Gekkonidae, but recent molecular work have placed Pygopodidae within Gekkonidae making it paraphyletic. These analyses have shown support of Pygopodidae and Carphodactylidae being sister taxa, with Diplodactylidae occupying a basal position in Pygopodoidea.

Below is a taxonomic list of pygopodoid genera in taxonomic order: