The Gilbert’s potoroo (Potorous gilbertii) is one of Australia’s most critically endangered mammals with a current estimated population of 70 individuals. Both the wild and captive populations have a long history of balanoposthitis with associated crusting, ulceration, and preputial discharge. We sought to identify the microbial species found in the discharge, determine their significance in causing balanoposthitis, and correlate these findings with reproductive success and survivorship. Bacteriologic examination revealed the discharge to be a polymicrobial infection involving Treponema spp., Actinobacillus spp., and Pasteurella spp. Preputial histopathology reported a moderate, chronic, erosive inflammatory response with diffuse, moderate to marked secondary epithelial hyperplasia in conjunction with moderate numbers of spirochetes, suggesting a causative relationship. Clinical examination, preputial biopsies, and serologic screening found no evidence of associated systemic disease. The clinical investigation of Treponema is significant with respect to the overall recovery of Gilbert’s potoroo, given the clinical and histopathologic similarities to Treponema paraluiscuniculi found in rabbits, causing dyspareunia, and the severity of the associated balanoposthitis.