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We report the discovery of a new species of doglike bat (Peropteryx) from the lowland Amazonian forests of Ecuador and Peru. It has transparent wing membranes that are faintly tinged brown with pale-brown arms and digits; ears that are separated on the forehead; and a skull with small, shallow pterygoid pits that are anterolateral to an undivided basisphenoid pit and that are separated by a mesopterygoid extension. These characters distinguish the new species from morphologically similar species with which it was previously confused (P. leucoptera and P. macrotis). A molecular phylogenetic analysis of unlinked loci from each of the four genetic transmission systems of mammals (mitochondrial, nuclear-autosomal, X, and Y chromosomes) independently corroborated the placement of the new species as the sister taxon to a clade that includes P. kappleri, P. macrotis, and P. trinitatis; the basal lineage for the genus is P. leucoptera. This phylogeny suggests that transparent wings (sometimes described as “white” but actually lacking pigment), the traditional character used to diagnose Peronymus, is not a unique synapomorphy. Furthermore, based on a molecular dating analysis, the depth of divergence of Peropteryx is equivalent to that of another New World emballonurid genus (Balantiopteryx). Therefore, Peronymus does not warrant higher-level recognition as a subgenus or genus.