Southern River terrapins (Batagur affinis) are among the most critically endangered turtles in the world. To augment the Cambodia population, a head-start program was established for the endemic subspecies Batagur affinis edwardmolli in 2006, and in 2015, prerelease health assessments were performed on 70 subadults (hatch years, 2006–2011). Combined choanal/cloacal swab samples (n = 70) were collected and screened by polymerase chain reaction (PCR) for Mycoplasma, herpesvirus, and ranavirus. Cloacal samples (n = 50) were also collected and cultured for Salmonella sp. Of 70 tested samples, six (8.6%) were positive for Mycoplasma, and all other PCR and culture test results were negative. Phylogenetic analysis of the 16S ribosomal RNA gene placed the Mycoplasma sp. from B. affinis edwardmolli in the chelonian Mycoplasma cluster that groups within the Mycoplasma pulmonis clade. This mollicute was not associated with clinical disease (defined as observable clinical abnormalities, such as depression, lethargy, respiratory signs, and anorexia) and is likely part of the endemic microbial flora of these terrapins.