Single nucleotide polymorphisms (SNPs) are the most widespread form of sequence variation encountered in genomes, and they hold great promise for elucidating the genetic characteristics mammalian populations (Morin et al, 2004). However, the difficulty and expense associated with SNP discovery in non-model species has hampered their wider implementation in conservation projects. Rapid advances in sequencing and genotyping technologies means large numbers of SNPs can now be interrogated simultaneously for relatively low cost in numerous model and domestic organisms, including the domestic horse (Equus caballus), using whole-genome genotyping arrays (Steemers et al, 2006). The application of SNP genotyping platforms across species boundaries presents a simple route to marker discovery in taxa sharing a recent evolutionary history. In this way genome-wide markers may be readily ascertained in non-model species, and high-quality genotyping data may be generated cheaply and efficiently in many individuals (Ogden et al, 2012). Samples from the order Perissodactyla (n=106) have been genotyped on the EquineSNP50 and SNP70 Beadchips. We identified 3028 domestic horse SNP sites (4.1% of sites interrogated) genotyping as polymorphic within at least one non-horse Perissodactyla species. A case study investigating the power of these newly discovered SNPs to predict kinship and parentage was undertaken in two endangered equid species. Przewalski’s horse (Equus przewalskii) and Persian onager (Equus hemionus onager) samples with known ancestry were genotyped to evaluate the correlation between marker and pedigree-based estimates of relationship. A pruned set of informative SNPs revealed a strong correlation between molecular and genealogical kinship for Persian onager (r =0.85-0.96). More variable correlations were reported for Przewalski’s horse (r =0.50-0.92). Simulations suggest as few as 50 highly polymorphic SNPs will provide sufficient power for paternity assignment with 95% confidence in both species. These results indicate a relatively small panel of SNP markers could be used to clarify pedigree relationships and parentage, providing a valuable resource for zoological institutions managing captive populations.