The characterization of freshwater mussels (Bivalvia) through morphological variability between and within sexes of the same species (Margaritifera margaritifera L.) is not possible due to morphological similarities. Classic morphometric measurements (e.g. shell length, shell width, shell height) are not sufficient to determine sexes within species. Thus, outline-based geometric morphometric analysis has been employed to characterize individual species, independent of its size. The study aimed to test the usefulness of this geometric morphometric tool to analyze shell shape divergence between and within sexes of freshwater mussel Margaritifera margaritifera L. A total of 75 landmarks were established for the outline curveof the outer shell contour of the mussels. Principal Component Analysis (PCA) revealed that components 1, 2, 3, and 4 provided significant summary of the characteristics of freshwater mussels and relative warp analysis will visualized shape variations by the transformation of grids. Relative warps 1 and 3 showed shape variations in the left shell valve and right valve for females and males at p-value <0.000. These shape variations may be attributed to the kind of habitat, feeding habits and inhabit a variety of substrates. Shape variations will also be attributed to the reproductive capacity of mussels that may affect the external morphology.Shape elongation of mussel is considered as a function of environment and shell obesity is influenced by individual growth.