Pond Turtle Shell Disease is an emerging threat to freshwater turtle populations, characterized by ulcerative and progressive shell lesions. The fungal pathogen Emydomyces testavorans, formally described in 2019, is the only species currently recognized within the genus and is known to infect multiple turtle species, including Trachemys scripta and Actinemys marmorata. Recent diagnostic submissions from freshwater turtles across the United States, however, have revealed a genetically distinct lineage of Emydomyces associated with similar shell lesions. Sequencing of the Internal Transcribed Spacer 2 (ITS2) region demonstrates only 90.56% similarity to E. testavorans, strongly suggesting the presence of a previously undescribed and potentially widespread pathogenic species. To formally characterize this novel species, we will isolate the fungus from infected shell tissue and conducted whole-genome sequencing and assembly. Comparative genomic analyses will be performed between the new Emydomyces species, E. testavorans, and other major reptile fungal pathogens, including Ophidiomyces ophiodiicola and species of Nannizziopsis. These comparisons enabled the identification of shared genomic features potentially associated with reptile host adaptation, keratin degradation, and pathogenicity. Preliminary analyses indicate that the new species forms a distinct phylogenetic lineage within Emydomyces, with genomic traits that may explain its ability to infect multiple freshwater turtle hosts across broad geographic regions. This work provides the first formal description and genomic characterization of a second species within Emydomyces. These findings expand our understanding of reptile-associated fungal pathogens and highlight the need for continued surveillance, improved diagnostic tools, and further studies on host susceptibility and environmental drivers facilitating disease emergence.