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The Peruvian sphaerodactyl gecko, Pseudogonatodes barbouri, is among the smallest reptile species in South America. Morphological information about this species, or even the genus, is limited. In this study, we produced a bone-by-bone description from the skull and atlantoaxial complex to contribute new phenotypic information about this poorly known lizard. To achieve this objective, we employed a divide-and-conquer approach in which each author digitally isolated one or two bones from the skull and produced a written description of these elements, thereby reducing 3D imaging processing and description to a fraction of time. In addition to a reduced phalanx in the fourth toe of both the hand and foot, the genus is characterized by having nasal bones with a broad lateral wing, an ectopterygoid that clasps the pterygoid, and an anterior shifting of the paroccipital process and as consequence the position of the quadrate, and squamosal not participating in the quadrate suspension. There are also modifications in fenestration and foramina and a trend towards synostosis of the jaw bones (e.g., coronoid + splenial, compound bone + surangular). Pseudogonatodes bears four long processes on the intercentrum of the axis; which is a character of New World sphaerodactyls.