Phylogenetic relationships of a sample comprising 248 bats belonging to 19 species and four families (Hipposideridae, Rhinolophidae, Molossidae and Vespertilionidae) from Senegal (Western Africa) were investigated with the use of multi-locus sequence data and non- differentially stained chromosomes. The karyotypes of Hipposideros ruber, H. tephrus, H. jonesi and H. cyclops were described for the first time. The standard Hipposideros formula was recorded in H. tephrus, H. jonesi and H. ruber (2n = 32, FNa = 60, FN = 64). The karyotypes of H. cyclops (2n = 36, FN = 66) and H. gigas (2n = 52, FN = 64) substantially diverged from this typical chromosomal complement. Rhinolophus landeri and R. fumigatus shared the same diploid number (2n = 58), but differed in the chromosome morphology (R. fumigatus - FNa = 60, FN = 64; R. landeri - FNa = 64, FN = 68). Rhinolophus landeri was found karyotypically distinct to other African populations, thus signalling a possible presence of cryptic forms within this species. The karyotypes of Chaerephon pumilus and Mops condylurus had a 2n = 48, FN = 54 and were similar to other previously studied species of this chromosomally conservative family. Chromosomal, Bayesian, maximum likelihood and genetic distance analyses revealed an indication for the existence of cryptic...