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The ten extant species in the genus Equus are separated by less than 3.7 million years of evolution. Three lines of investigation were pursued to further characterize equid genome organization. 1.) The Przewalskis wild horse (E. przewalskii, EPR) has a diploid chromosome number of 2n=66, while the domestic horse (E. caballus, ECA) has 2n=64. A comparative gene map for E. przewalskii was constructed using 46 bacterial artificial chromosome (BAC) probes previously mapped to 38 of 44 E. caballus chromosome arms and ECAX. BAC clones were hybridized to metaphase spreads of E. przewalskii and localized by fluorescent in situ hybridization (FISH). No exceptions to homology between E. przewalskii and E. caballus were identified, except for ECA5, a metacentric chromosome with homology to two acrocentric chromosome pairs, EPR23 and EPR24. 2.) The onager (E. hemionus onager, EHO) has a modal diploid chromosome number 2n=56 and a documented chromosome number polymorphism within its population, resulting in individuals with 2n=55. Construction of a comparative gene map of a 2n=55 onager by FISH using 52 BAC probes previously mapped to 40 of 44 E. caballus chromosome arms and ECAX identified multiple chromosom