Chemosynthetic ecosystems are scattered in the deep ocean, harbouring highly specialized communities, among which the degree of connectivity and dispersal is scarcely studied. This gap is largely due to limited range distribution, either real or due to highly partial exploration, preventing the availability of a sufficient number of samples for population genetic analysis. For the few species that escaped this gap, large-scale panmixia was often reported, raising wonders as to the evolutionary mechanisms involved in the first steps of speciation. Vesicomyid bivalves are one of the most abundant groups of chemosynthetic fauna, for which depth was proposed as an essential driver of differentiation. Early stages of speciation are thus expected to involve genetic differentiation along depth gradients. The vesicomyid bivalve Christineconcha regab was studied across widely separated localities along the Western African margin, from the cold-seeps of Regab pockmarks located at 3150 m depth on the Congo margin to the turbiditic lobes of the Congo deep-sea fan located at 5000 m depth, using mitochondrial (COI) sequences and eight microsatellite loci. Despite rather high density in relation to high organic matter availability, results obtained showed rather low levels of genetic diversity at both mtDNA and microsatellites. The main consistent pattern of differentiation was observed across depths from Regab pockmark (South-Western part) and lobe areas (Lobe B and C). This is likely due to the largest sample sizes characterizing Regab_SW and Lobe C allowing the detection of faint genetic differentiation, and possibly to a stronger signature in the demographically declining (thus acknowledgedly under sampled) Lobe B. Other significant results were not congruent among markers, suggesting low statistical power due to limited sample size or the occurrence of chaotic genetic patchiness. Altogether, the results suggest the occurrence of effective gene flow at regional scale, and departure from equilibrium in the recently discovered lobes of the Congo River, possibly resulting from unstable environmental conditions and recurrent events of extinction recolonization.