We analyzed the karyotypes of the Formosan muntjac (Muntiacus reevesi micrurus) including G-banding, C-banding, and NOR-staining analyses. The results showed the species has a 2n = 46 chromosome complement. The G-banding patterns as well as the localizations of rRNA gene clusters and constitutive heterochromatins were similar to those of Chinese muntjac (M. reevesi reevesi). In addition, satellite DNA analysis was also carried out. The restriction periodicity of FM-satI revealed a 0.75-kb register indicating that this deer species belongs to the plesiometacarpalia division. Finally, the FISH study demonstrated that the Formosan and Chinese muntjacs have similar localizations of satellite I DNA in their respective genomes. Although the Formosan and Chinese muntjacs share almost identical results of cytogenetic analyses, Southern blot and FISH studies revealed some sequence divergence of satellite I DNA between these 2 species supporting the classification of the Formosan muntjac as a subspecies of, not the same species as, the Chinese muntjac. Furthermore, the data suggest that satellite I DNA of the Formosan muntjac and that of the Chinese muntjac may have originated from different ancestral sequences or that they may have experienced different homogenization patterns in the course of evolution.