The unsolved systematics of the genus Cardiomya has led to a sequence of astonishing identification mistakes. This scenario is a result of the rarity of specimens and, more importantly, the lack of knowledge about which characters are relevant to the genus taxonomy. In this study, we developed a method based on standard linear discriminant analysis to identify the smallest number of morphological characters that efficiently distinguish individuals at the species level of Brazilian Cardiomya. Starting from 29 morphometric measurements obtained from photographed Cardiomya shells, we were able to identify only five characters: the dorsal inflection of the rostrum, the distance from the posterior most rib end to the umbonal posterior margin and the distance from the central point of the valve to the anterior margin at 45°, 15° and −30° angles. Surprisingly, all these characters are related to the shell outline and not the ornamentation, which is a remarkable character in Cardiomya. We performed a one-way ANOVA with post-hoc Tukey HSD test specifically using the total number of ribs to verify its discriminant power in species identification. Our analysis demonstrated that the number of ribs does not show a significant difference between the analysed species.