Non-tuberculosis Mycobacterium spp. infections are a serious threat to both fish and human health. Mycobacterium infections cost the aquaculture industry millions of dollars in losses annually. Difficult to treat and eradicate, fish stocks infected with these bacteria are typically destroyed and the systems decontaminated. Besides being costly in commercial operations, such strategies are impractical for use in endangered species work, as there are often limited quantities of broodstock available. A Mycobacterium species has been presumptively identified in elderly fish that showed granulomas and histological characteristics of mycobacterial infection. Mycobacterium has also been recovered from several sample types from Devils Hole, including Spirogyra, amoebas, cyanobacteria, Hydrobiid Snail (Tryonia) and Dytiscid Beetle (Neoclypeodytes). Mycobacterium-targeted therapies have demonstrated potential for creating specific-pathogen-free lines. These lines could allow for investigation of the intricacies of larval developmental physiology and functional genomics without the confounding effects of chronic disease burdens. 16S rRNA sequencing of the recovered Mycobacterium species is underway to determine if the species found in hybrid Devils Hole pupfish are the same as those recovered from Devils Hole. Understanding the relationship of these species, as well as identifying the environmental reservoirs in Devils Hole can provide insight into how these species may be impacting the health of fish in Devils Hole.