Ambystoma mexicanum belongs to the family Ambystomatidae. It is one of the 30 species of the genus Ambystoma, which lives in a wide geography from southern Mexico to southern Alaska. It is accepted as a model organism in evolutionary biology, developmental biology, and regenerative medicine research. It can regenerate the brain, heart, and kidney organs as well as limb regeneration. Accurate identification of the model organism is important for the reproducibility and comparability of experiments. We aimed to confirm the species identification of axolotls using integrated taxonomic methods that were grown at Mersin University Aquaculture Units of the Faculty of Fisheries. Cytochrome oxidase subunit 1 (COI) and cytochrome b (Cytb) gene fragments of mtDNA sequences were used as molecular markers for phylogenetic analyses and species delimitation methods and compared with the sequences that were submitted to NCBI GenBank as species of Ambystoma. In the analyses that were conducted with different data sets, the individuals in question were grouped as a candidate species with the A. mexicanum species whose sequences were given in previous studies. All sequences obtained in this study and A. mexicanum sequences obtained from NCBI GenBank were grouped as haplotypes and their genetic distances were found to be 0 and it was determined that the individuals which were the subject of this study definitely belong to the A. mexicanum species. The results revealed that some species within the genus Ambystoma, especially A. barbouri and A. texanum, may be species complexes. On the other hand, A. mexicanum was grouped together with A. andersoni as candidate species in all analyses performed with the combined datasets of COI, Cytb, and COI+Cytb. These results revealed that the taxa in question are paraphyletic and should be assigned to the A. mexicanum species.