Munida subrugosa and M. gregaria are very abundant in the southern hemisphere, especially off New Zealand and South America. The specific identity of both species is still controversial and accurate identification is needed for conservation or ecological purposes. In this study we used univariate and multivariate methods to determine the morphological differences between both species/morphs. Analyses of covariance of ten morphological variables regressed individually on the carapace length demonstrated that the carapace (including rostrum) and eyestalks (EL) were longer, and the anterior carapace (ACW), the rostrum basis (RBW), and dactylus (DaW) and propodus (PW) of the third maxilliped were wider in M. gregaria than in M. subrugosa. In contrast, the carapace, mandible and eyestalk were wider and the rostrum was longer in M. subrugosa compared to M. gregaria. A stepwise discriminant analysis found that five body measurements namely DaW, EL, PW, RBW and ACW, were useful to discriminate between both species/morphs. The difference between the two discriminant functions provides an objective decision rule for the classification of both species/morphs. We also present the linear relationships of wet and dry masses on size, for use in biomass estimations of Munida spp. as prey.