Abstract The genus Rhinophylla Peters, 1865 (Carolliinae: Phyllostomidae) comprises three species: R. pumilio Peters, 1865, R. fischerae Carter, 1966 and R. alethina Handley, 1966. Only the first two species have been cytogenetically studied to date. Previous studies on specimens of Rhinophylla fischerae from two populations from East of Andes (Colombia) showed the karyotype with 2n=34 and FN=56. In this paper, we report the results of cytogenetic analysis of six specimens of Rhinophylla fischerae from Brazil. Probably chromosomal differences can be found among the populations because of the geographic distance. Metaphase chromosomes were obtained in the field by direct extraction of bone marrow. The metaphases were analyzed by conventional staining, G- and C-banding, NOR-staining and FISH with telomeric probes. Rhinophylla fischerae has 2n=38 and Fundamental Number FN=68, with small amounts of constitutive heterochromatin in the centromeric regions of the chromosomes and the long arm of pair 16. Fluorescence in situ hybridization using telomeric probes did not show any interstitial sequences. Hybridization with human 18S and 28S rDNA probes and silver staining revealed the presence of Nucleolar Organizer Regions at the long arms of pairs 16 and 18. The pattern of G-banding showed that this population had a huge chromosome variation compared with previous studies on specimens of Rhinophylla fischerae. The chromosomal differences among populations that have been morphologically classified as R. fischerae suggest that this species should be considered a cryptic species complex, and that the populations from different geographical regions analyzed to date should be considered species of this complex, where the chromosomal rearrangements had key importance.