In recent years several new sportive lemur species (genus Lepilemur) have been described. In contrast to other lemur taxa, the genus shows comparatively high chromosomal variability, which, in addition to molecular data, can be used to infer phylogenetic relationships within the genus. By comparing R-banding patterns and fluorescence in-situ hybridization data, we detected chromosomal rearrangements that occurred during speciation within the genus. The analysis of these data with cladistic methods resulted in a dichotomic phylogenetic tree comparable to that obtained from mitochondrial sequence data. However, a phase of reticulation can not be excluded from the evolution of Lepilemur. Although some incongruences were detected, both phylogenies show similar patterns concerning relationships of the basal and terminal splits. We therefore hypothesize that both, chromosome rearrangements and molecular mutations, alone or in combination, contributed to the speciation process in sportive lemurs.