Domestication of animals and plants marked a turning point in human prehistory. To date archaeology, archaeozoology and genetics have shed light on when and where all of our major livestock species were domesticated. Phenotypic changes associated with domestication have occurred in all farm animals. Coat colour is one of the traits that have been subjected to the strongest human selection throughout history. Here we use genotyping of coat colour SNPs in horses to investigate whether there were any regional differences or preferences for specific colours associated with specific cultural traditions in Iron Age Sweden. We do this by identifying the sex and coat colour of horses sacrificed at Skedemosse, Oland (Sweden) during the Iron Age, as well as in horses from two sites in Uppland, Ultuna and Valsgarde (dated to late Iron Age). We show that bay, black and chestnut colours were all common and two horses with tobiano spotting were found. We also show how the combination of sex identification with genotyping of just a few SNPs underlying the basic coat colours can be used to identify the minimum number of individuals at a site on a higher level than morphological methods alone. Although separated by 500 km and from significantly different archaeological contexts the horses at Skedemosse and Ultuna are quite homogenous when it comes to coat colour phenotypes, indicating that there were no clear geographical variation in coat colouration in Sweden during the late Iron Age and early Viking Age.