Omani Jabal Akhdar goats are highly valued for their resilience, superior growth rate and twinning rate compared to other Omani goats. Therefore, understanding their genetic diversity and population structure is imperative for sustainable breeding efforts and conservation of the breed. This study aimed to assess the genetic diversity and population structure of Jabal Akhdar goats by genome-wide nucleotide polymorphisms (SNPs) using the Illumina 50K Goat Chip. Multidimensional Scaling Analysis (MDS) and Admixture analysis revealed that Jabal Akhdar goats has a distinct genetic ancestry that is a mixture between the Asian and African goat lineages which highlights the historic maritime trading and activities of the Omanis with both continents. The MDS analysis and the Reynolds unweighted distances both showed that the Jabal Akhdar goats share a close genetic ancestry with West Asian breeds such as Iranian Bezoar, the Australian Cashmere breed, and Turkish goats such as the Kil breed, all of which are adapted to cold climates and high elevations. Notably, the breed exhibited a reasonable inbreeding level (0.219), comparable to other West Asian breeds, indicating adequate levels of genetic diversity. This study represents the first genome-side characterization of the Jabal Akhdar goats breed. Despite its moderate inbreeding levels, attention should be focused on conservation efforts to safeguard the distinctive genetic diversity of Jabal Akhdar goats to prevent the erosion of its genetic diversity or admixture with exotic commercial breeds.