Global climate change and associated temperature increase in the marine environment will affect the condition of all marine organisms. We present the first experimental investigation into the response of an epidermal microbiome to acute temperature shifts in a cartilaginous vertebrate species. Here we used shotgun metagenomics to describe the epidermal microbial communities of Triakis semifasciata (leopard sharks) exposed to an acute temperature shift from a cool (15˚C) and warmer (21˚C) temperature. While our findings reveal significant changes in both the taxonomic and functional gene profiles of the epidermal microbiomes occurred as an initial in response to temperature shifts, the overall structure and diversity of the communities stabilized with time. The relative abundance of key microbes, including Sphingopyxis, Halomonas, Ralstonia, Erythrobacter, and Sphingomonas decreased with increasing temperature. While significant increases in relative abundance of Colwellia, Flavobacteriia, and Flavobacterium were observed in the increased temperature group. The reduction in heat stress proteins within the microbial community suggests a rapid loss of the microbes with these genes that was surprising. This suggests a form of community stabilization and functional adaptation with major shifts in dominant taxa, resulting in an initial vulnerable period of the host to acute environmental changes.