Goats were raised in different regions of the world for various purposes including milk and meat production as well as skin and fiber. The number of goats evaluated to be about 2.5 million heads, which represent about 30% of total meat income of Saudi Arabia. Saudi local goat breeds did not receive the required attention about their genetic information, despite their important adaptive characteristics. This study aims to access genetic diversity of some Saudi goat breeds depending on sequence analysis of specific mitochondrial D-loop region. Results showed that the Saudi goats resemble two main groups (1 and 2). Group one, is classified into two subgroups. Subgroup 1a (Saudi goats with accession numbers MG725669, MG725670 and MG725673 of Habsi breed) and Subgroup 1b (Saudi goats with accession numbers MG725674, MG725676 and MG725677 of Harri breed). Lineage A (group one), showed characteristic difference compared to all other studied goat members around the world. The nearest goat to this Lineage is goat accession number (KJ940969). On the other hand, Saudi goats outside this group (group 2) showed high similarity with other sequences of goats obtained from GenBank database, which included in this study. The results of Lineage 2 (group 2) showed no noticed sharp difference with the published GenBank database sequences. Finally, Lineage 1(group one) showed novel results including specific SNPs and one deletion, which is characteristic only to this group. This will give more insights about correlation between sequence, classification and function of these breeds.