Bandicoot rats are a widespread species in Asia. Throughout their distribution, bandicoot rats are of high sanitary importance as reservoirs of at least 10 human diseases. In mainland Thailand, Cambodia, Laos, and Vietnam, where two species coexist, taxonomic distinction based on external characters is difficult and may lead to a certain proportion of misidentification. The purpose of this paper is to evaluate the efficiency of classical methods for distinguishing these bandicoot species, and provide new, simple, and cheap tools for discriminating species based on molecular characteristics, morphological ratio, and morphometric variation. Two PCR tests were developed: a first (PCR1) for distinguishing Bandicota and Rattus genera, and a second (PCR2) for distinguishing Bandicota indica and Bandicota savilei species. We evaluated two morphometric approaches for species discrimination: (a) one based on the ratio between head and body and hind-foot length, and (b) a second based on landmark analysis of mandible forms. The accuracy of both morphological approaches was fairly high. Together, the three identification tools appear useful for a wide scientific community, including curators, agronomists, ecologists, and epidemiologists wishing to have access to reliable species identification.