The major objective of studying the biodiversity of Syrian Arabian horses was to identify the population structure in a set of Syrian Arabian horses representing the three major strains. For the study, we used different genetic markers. The variability of endurance and morphological traits are beneficial in breeding programs. We tested genome-wide associations (GWAS) to find a causal relationship between morphological traits and genetic variants. Furthermore, we used the candidate gene approach to investigate the variability of genes contributing to endurance performance.