Despite their well-developed limbs, molecular phylogenies have demonstrated that Carphodactylidae is the sister group to Pygopodidae, a highly specialized family of legless lizards.

[8] A morphological phylogenetic analysis by Bauer (1990) generally supported Kluge’s classification scheme, though the internal relationships of carphodactylin species were very different.

[9] Summary of Kluge's classification scheme:[8][9] Pygopodinae Diplodactylini Carphodactylus Phyllurus Nephrurus Pseudothecadactylus Rhacodactylus Eurydactylodes Bavayia Naultinus Hoplodactylus Heteropholis

[13] Simplified results of Donnellan et al., 1999, focusing on Australasian geckos:[13] Pygopods Nephrurus Carphodactylus Rhacodactylus Pseudothecadactylus Diplodactylini Carphodactylidae, in its present-day usage, was codified by Han et al. (2004).

The family Pygopodidae was basically restricted to the legless pygopodines, and subsequent studies would rename the Australasian radiation to Pygopodoidea or Diplodactyloidea.

[2][3] Shared morphological traits are scant, but the two families both have an unusually complex squamosal with its lower end wrapping around the rear branch of the parietal.

[3] Simplified results of the combined nuclear and mitochondrial analysis of Oliver & Bauer, 2011:[2] Diplodactylidae Pygopodidae Carphodactylus Saltuarius Phyllurus Uvidicolus Underwoodisaurus Nephrurus Simplified results of Skipwith et al., 2019:[3] Diplodactylidae Pygopodidae Orraya Saltuarius Phyllurus Carphodactylus Uvidicolus Underwoodisaurus Nephrurus