The origin of the Coldblooded trotter (CT) provides a unique opportunity to identify genes influencing racing performance. The CT originates from the North Swedish draught horse (NS) and these two breeds retain high levels of genetic similarity (Fst = 0.08). However, prior to the introduction of paternity testing in 1969, crossbreeding with the Standardbred (SB) was used to improve CT performance. We hypothesize that the gains in CT performance over the last 50 years may in part be explained by the maintenance of favorable genetic variants originating from the SB. As such, the aim of the current study was to compare the genetic makeup of these three breeds and to identify genetic footprints of athletic performance. A sliding window Delta Fst analysis was performed across all breeds using data generated from the equine SNP50K array (CT, n=11; NS, n=19; SB, n=12). Five key regions were revealed where the CT and SB were genetically similar, but together differed from the NS. Seven genes reside in these segments, some of which affect muscle metabolism, such as regulation of cell growth in response to nutrient and mitochondrial DNA function in muscle. Genotyping of the top four differentiated markers in additional CT (n>130) showed that two were significantly associated (p<0.05) with performance traits, e.g. number of victories and time records. Additional genotyping will now be conducted in diverse racing breeds to ascertain the importance of these variants, and the current study will be augmented with additional Delta Fst analysis using whole genome sequence data.