The hermit crab Clibanarius signatus Heller,1861, inhabits varied intertidal habitats of the Red Sea coast, such as rocky shores and mangrove littoral salt marshes. Shield-shape variation among three populations of C. signatus was analyzed with geometric morphometric methods. Shape variation was studied through multivariate analyses using configurations aligned by the generalized Procrustes analysis. Shape variation was explored through principal component analysis. The ordination of the populations and the sexes was investigated using discriminant analysis of canonical variables. Centroid size, as a measure of overall size, was used to estimate size variation among the three populations and the sexes. The results revealed the presence of shield-size variation among the three populations and confirmed the size sexual dimorphism in two populations. Moreover, the analysis revealed the occurrence of two morphotypes based on a covariation between shield shape and shape of occupied shells. The geographic distance was not a good predictor of shield shape. Cross-validation analyses correctly reclassified more than 70% of individuals and 66% of sexes to their correct group. It was suggested that association in shield-shell shape could be the result of the phenotypic plasticity of this species.