Available ecological information, an extensive distributional range, conflicting osteological data, and a proposed early Miocene origin provide the impetus for the present study which investigates genetic structuring, biogeographic, and phylogenetic relationships within the Aplocheilichthys spilauchen lineage. Through the analysis of the mitochondrial gene COI, species delimitation methods (ABGD, GB, GMYC, bPTP) were applied, recognizing 6–7 OTUs with absolute pairwise genetic distances ranging between 8 and 22%. The onset of diversification is estimated to be within the middle Miocene and both dispersal and vicariance-shaped A. spilauchen diversity and distribution, as suggested by time-calibrated and ancestral range reconstruction (S-DIVA) analyses. We report for the first time, a pattern of diversification within a lineage of brackish water fish that is concordant with the historical distribution of coastal mangroves forests, shaped by a series of historical events that likely affected forest cover since the middle Miocene (e.g. major climate shifts and sea-level fluctuations, onset of the modern Congo River outlet, increased volcanism in the Cameroon Volcanic Line). Supplementary information The online version of this article (doi:10.1007/s10750-020-04497-3) contains supplementary material, which is available to authorized users.