Twenty-six captive individuals of the ellipsiprymnus subspecies group of Kobus ellipsiprymnus were found to have chromosomal complements of 2n = 50-52 (FN = 61-62), and 26 of the defassa subspecies group, including three specimens from Lake Nakuru National Park, Kenya, had complements of 2n = 53-54 (FN = 62). G-banded karyotypes that were numbered according to the standard karyotype of Bos taurus revealed that variation in diploid number was the result of polymorphism for two independent centric (Robertsonian) fusions. The ellipsiprymnus group was polymorphic for a 7;11 centric fusion. Both elements of chromosome pairs 7 and 11 were fused in fusion homozygotes (2n = 50); in fusion heterozygotes (2n = 51), only one element of each pair was fused. The 7;11 fusion was lacking in specimens with 2n = 52. The defassa group was polymorphic for a 6;18 centric fusion; individuals were either heterozygous for the fusion (2n = 53) or lacking it (2n = 54). There were no defassa group individuals that were homozygous for the 6;18 fusion (2n = 52), but this may be a sampling artifact. The 6;18 fusion was fixed in the ellipsiprymnus group, whereas the 7;11 fusion was absent in the defassa group. In G- and C-banded karyotypes, all autosomal arms and the X chromosomes of the two subspecies groups appeared to be completely homologous. However, the Y chromosome was acrocentric in the ellipsiprymnus group and submetacentric in the defassa group, possibly the result of a pericentric inversion. Fixed chromosomal differences between the two subspecies groups reflect a period of supposed geographic isolation during which time they diverged genetically and phenotypically, and the centric fusion polymorphisms raise the possibility of reduced fertility in hybrids. These data, in conjunction with phenotypic and mitochondrial DNA data, suggest to us that populations of the ellipsiprymnus and defassa groups should be managed separately.