Understanding how landscape structure shapes the genetic structure of populations of keystone species is important for their long-term management. We tested the unidirectional dispersal hypothesis on the linear river landscape of the Wouri River and the one catchment-one gene pool hypothesis on red mangrove (Rhizophora racemosa) populations of the Cameroon Estuary complex. Therefore, we conducted release-recapture experiments in the field, and sampled 649 adult trees for plant material for genetic analyses. This allowed for estimating genetic diversity and structure, as well as dispersal directionality. Genetic diversity in populations downstream did not differ significantly from upstream populations and the molecular variance of populations did not correlate with their position on the linear landscape. Contemporary and historical migration estimates indicated bidirectional dispersal, i.e. in both the downstream and the upstream direction along the Wouri River. This was confirmed by the propagule dispersal directions derived from our field experiments. Bayesian clustering analysis assigned all individuals of this estuary into one cluster, suggesting high inter-catchment connectivity. River flow currents, tides, and wind plausibly operate together to ensure the high genetic connectivity within this complex estuary.