This publication uses and presents R routines that perform various morphometric analysis in the context of rodent systematics. The morphological variation of two commensal rat species, Rattus exulans and Rattus tanezumi, is analysed and the potential for discrimination between the two is assessed. Specimens were trapped in three localities of Northern and North-Eastern Thailand. Shape and size variation are analysed in regards to sex, species, and geographical effects with various morphometric methods: log-shape ratios on body measurements, elliptic Fourier analyses on teeth outlines, Procrustes superimposition on skull coordinates. Both species are significantly different; however, the discrimination seems to be better on skull Procrustes coordinates and on teeth size than on other morphometric data set. Where different allometries exist between species and where species differ in size and shape, it is shown that filtering allometry using the approach of Burnaby (1966) can improve the discrimination between species. Sex size and shape dimorphism is reduced by comparison to interindividual variation. Shape variation varies between sampled localities for Rattus exulans, this is not the case for Rattus tanezumi. This pattern is possibly related to the more commensal life of R. exulans.