The Common Mustached Bat (Pteronotus parnellii) is a mormoopid bat living in caves in lowland rainforests throughout the north and eastern Neotropics, including several Caribbean islands. Recent studies have shown that this taxon is certainly a composite of several cryptic species, especially in the western part of the Guiana Shield, where molecular reconstructions and bioacoustics point to the presence of at least two cryptic species that may not be related to genuine P. parnellii, native of Jamaica. The current taxonomy of this species complex is therefore confused. We examined here over 200 bioacoustically identified individuals to show that two phonic types live in sympatry in French Guiana with no overlap in frequencies of echolocation calls. Morphologic variation showed consistent and significant differences between the two phonic types, but external measurements were unable to discriminate all bats. Two mitochondrial markers analyzed in a selection of each of these phonic types were further used to evidence that they represent two genetically discrete groups, and to assign them to the existing molecular clades described elsewhere. Molecular comparisons with reference specimens sampled near the type localities of P. parnellii and P. rubiginosus further suggest that the 53 kHz phonic type found in French Guiana and Amapa (Brazil) should be assigned to the later species, while the 59 kHz phonic type represents an undescribed species.