Mangrove clams of the genus Geloina primarily inhabit mangrove ecosystems and hold significant ecological and economic values. Accurate species identification among Geloina species is challenging because the members share similar morphological characteristics. In this study, a multivariate morphometric analysis of 13 conchological traits was performed based on a molecular systematic framework to find the differences between Geloina coaxans and Geloina erosa from four major mangrove areas on Hainan Island: Tielugang in Sanya, Dongzhaigang in Haikou, Qinglangang in Wenchang, and Hongshuiwan in Chengmai. Analysis of variance and principal component analysis revealed three traits (categorized as hinge teeth) with significant differences between the two species, which were then used for subsequent cluster analysis and discriminant analysis. Cluster analysis could clearly distinguish the two species. Although within the populations of G. coaxans, the one from Haikou exhibited the greatest morphological divergence from the other three populations. A discriminant function was established for distinguishing G. coaxans from G. erosa, with an overall discriminant accuracy of 87.9%. This study indicates that multivariate morphometric analysis may help identify the two species under a clear molecular systematic framework.