Stingrays are common along shorelines, where they occupy shallow soft bottom habitats. Stingrays prey on benthic invertebrates like bivalves, polychaetae worms and crustaceans. They preyed upon by larger organisms, usually other elasmobranchs. Stingrays host an abundance of microbial symbionts, including bacteria, archaea, and viruses, which make up their microbiome. Stingrays are dorsally ventrally flattened to live in the benthic environment and the microbiome could be influenced by either the microbes in the water column or on the sediments that cover the surface of the organism. Their skin is covered by a mucus layer which is a dynamic and unique to each species of ray. Here we aim to categorize the taxonomic and functional gene composition of the skin microbiome using shotgun metagenomics. We compared the microbiomes from two species, the round stingray, Urobatis halleri, and bat ray, Myliobatis californica and found a significant difference (PERMANOVA p = 0.001). We determined that microbiomes differ across two locations (Los Angeles and San Diego) in California (PERMANOVA p = 0.011). SIMPER analysis revealed a 15.84 % average dissimilarity between the two species. Bat rays had greater intraspecies variation (82.67% similarity) compared with round rays (88.56% similarity). Among the most abundant five taxa contributing to the differences is an unclassified Alteromonadales order, which will investigate further with metagenome assembled genomes. Therefore, the stingray microbiomes are species specific and novel, but there is local variance in the proportional abundance of some taxa.