Microbial genomes consist of both vertically and horizontally transferred genes, and genes are gained when microbes transfer into new environments, like invading a new host. We have investigated the microbes on the skin of Chondrichthyes (sharks and rays), which are the oldest extant vertebrate lineage and provide a pivotal point in vertebrate evolution. The increase in sequencing capacity and improvement in computational programs has enabled us to explore the relationships of microbial genomes across host phylogenies using Metagenomes Assembled Genomes. First, we identify genes that are overrepresented in the epidermal microbiome compared with the water column and we found that shark associated microbes lacked genes for nitrogen fixation, but gained genes for sulphur, phosphate, and heavy metal metabolism. Core and novel location-specific microbes were identified using MAGs from whale sharks collected from 5 locations around the world, these were distinct from the water column MAGs, suggesting shark specific microbial lineages. We are delving into the construction of MAGs from multiple shark species to investigate whether the reads are recruited to different genomes in proportion to the phylogenetic relationship of the sharks to explore microbial-host co-evolution.