The Ambystoma mexicanum axolotl is a highly threatened amphibian and a valuable research model, with very little information about bacterial diseases affecting it. The aim of this study was to perform an identification of bacteria responsible for septicemia in three individuals. For all of them, necropsies were made, bacteria classification was performed by traditional and DNA-based molecular methods and tissues were histologically examined. All animals showed edema and ascites, and other tissues such as the lungs, spleen, liver, and kidney were also affected, dermatitis also occurred, in one case, the dermatitis was severe. Two bacterial isolates showed genetic identities of 99% with Aeromonas veronii, one with Citrobacter freundii, and another with 100% identity with Citrobacter portucalensis. These and other Enterobacteriaceae species of Aeromonas genus have been reported to produce septicemia in Anura amphibians and fish, pointing out that they are a health hazard for aquatic animals. Future endeavors to determine these bacteria prevalence, the search for antibiotic resistance/susceptibility, factors that can trigger the pathology, and the development of early diagnostic tools should be done to improve our understanding.