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Pygopodids are limb-reduced, miniaturized geckos found across Australia and New Guinea. Pygopodids are mainly terrestrial; however, Aprasia species are highly fossorial and further miniaturized, converging on similar ecology and morphology to typhlopid snakes. Additionally, Aprasia from eastern/central and western Australia exhibit distinct skull shapes, possibly due to the functional demands of burrowing in different soil types. Another pygopodid genus, Ophidiocephalus, also was described as fossorial with morphology most similar to eastern Aprasia species, and thus may experience a similar pattern of cranial stress when digging. The burrowing mechanics of pygopodids have never been studied; however, we propose that mechanical stress is distributed outwardly as a shell across the expanded nasals, rather than along an anterior-posterior central column as suggested for other head-first burrowing squamates. To test how differences in morphology may be related to differing functional demands, Finite Element Analysis was implemented by applying and comparing both face loads and point loads of 20N onto 3D solid meshes of the skulls of one eastern/central and one western Aprasia, and one Ophidiocephalus. The resulting stress and strain were low in all taxa and appeared to be evenly spread out across each axis; however, Ophidiocephalus experienced slightly higher average stress than either Aprasia. Although anatomically divergent, each lineage appears to have independently converged on a similar level of biomechanical performance.