Animal genetic resources are an essential resource for pastoral and agropastoral civilizations for ensuring and improving the livelihoods of a substantial part of the population. Goats, with their diversification, contain traits that are becoming increasingly important as a result of climate change and worldwide population expansion. This project aimed at exploring the genetic diversity and population structure of Jabal Akhdar goats using genome-wide single nucleotide polymorphisms. This assessment is critical for future protection and preservation of its genetic diversity. Furthermore, research into population structure and genetic diversity is required to comprehend the significance of evolutionary processes and the current distribution of biodiversity in this unique and valuable breed. Samples were collected from Jabal Akhdar goats and genotyped using the Goat-Illumina 50K Goat Chip yielding 53,347 SNPs. The resulting genotypes were merged with the Adapt Map project genotypes to be able to compare Jabal Akhdar breed with other breeds around the world. Then, data quality control was performed to eliminate any unwanted SNPs or individuals unsuitable for the analysis. Several analyses were conducted such as Principal Component Analysis (PCA), STRUCTURE analysis, and genomic inbreeding analysis. Our results showed that the PCA, STRUCTURE, phylogenetic, Wright’s Fixation Index (FST) and "Estimates of Evolutionary Divergence over Sequence Pairs between Groups" analysis agreed that the Jabal Akhdar breed clustered close to West Asian breeds including Iranian, Pakistani, and Turkish goat breeds and that they had a similar genetic ancestry. The inbreeding level of Jabal Akhdar goat was 0.219, which is considered reasonable compared to the average of other West Asian breeds (0.227) and an indication of good genetic diversity in this breed. The FIS for Jabal Akhdar breed was 0.036, which is considered also reasonable compared to other pure breeds given that it is a pure non-crossbred breed that is geographically isolated from other breeds in Oman. Nevertheless, such levels of genetic diversity warrant caution and signify that this breed requires additional attention to preserve its genetic diversity at the current levels.