Littoraria snails are an important component of the food chain in the mangrove ecosystem. This study intends to examine the influence of the Western Indian Ocean currents and isolation-by-distance (IBD) on the genetic diversity and structure of Littoraria subvittata and Littoraria pallescens, which are the most dominant species of Littoraria along the East African coast. A fragment of the mitochondrial COI gene from 334 individuals of L. subvittata and 134 of L. pallescens collected from mangroves sites in Kenya, Tanzania, Mozambique and Madagascar, was used in the analysis. Low values of nucleotide diversity (L. subvittata: 0.13 ± 0.10%, L. pallescens: 0.12 ± 0.00%) and high to moderate haplotype diversity (L. subvittata: 0.57 ± 0.03, L. pallescens: 0.55 ± 0.05) were recorded for both species. An analysis of molecular variances (AMOVA) detected a significant genetic difference among populations of L. subvittata (Φst: 0.093, P < .001) and was supported by significant IBD, while L. pallescens showed panmixia (Φst: 0.004, P > .05). The spatial analysis of molecular variance (SAMOVA) did not detect population clusters in L. subvittata. In contrast, SAMOVA revealed slight but significant genetic structuring between two groups of populations in L. pallescens. These results may indicate that L. subvittata is sensitive to impacts of population geographic IBD compared to L. pallescens. The differences in genetic structure of populations between the two species may be linked to their larval potential differences in crossing the oceanic barriers such as currents and eddies during dispersal.