In the present study, shell morphological variations of the horse mussel species Modiolus philippinarum and Modiolus modulaides have been explored by the means of linear morphometrics for size and landmark-based geometric morphometrics for shape. Linear morphometrics revealed significant differences in shell length [t(298) = –6.29, p = 1.08 x 10–9), shell height [t(298) = 10.60, p = 1.74 x 10–22], shell width [t(298) = 2.13, p = 0.034], PAMS or posterior adductor muscle scar length [t(298) = 2.16, p = 0.032], hinge length [t(298) = 2.26, p = 0.025], umbo length [t(298) = –5.54, p = 6.73 x 10–8], and anterior length [t(298) = –5.59, p = 5.16 x 10–8] between species. However, upon the use of these morphometric characters to develop an index that will easily discriminate the species, only the relationships of shell length vs. shell width and hinge length were significant (ANCOVA, width/ length F = 18.45, p = 0.0001; hinge/length F = 7.76, p = 0.005) but an invariably high overlap between species was observed resulting in a 23.3% misclassification rate. Contrastingly, the analysis of shape variables through landmark-based geometric morphometrics revealed significant differences in shell shape between the two species [MANOVA, Wilk’s λ = 0.01, F(24,335) = 941.4, p = 3.47 x 10–291] with a 0.0% misclassification rate. Generally, M. modulaides were found to have an elongated shell while M. philippinarum was compressed and convex. Also, visualization through thin-plate spline expansion factor plots revealed that variability in shell shape between the species occurred mostly in the posterior and ventral region of the shell and was attributed to the species ecology. The findings of the present study encourage the use of geometric morphometric methods in species delineation, especially when ecotypes or sibling species are present.