In addition to density dependent (i.e., food availability) and independent (i.e., abiotic gradients) forces, size-selective harvests of organisms often induce changes on its life history, demography, and reproduction. Shellfish are increasingly overexploited worldwide and the effect of size-selective harvest on their populations is unclear. The African bloody cockle Senilia senilis is a dominant bivalve in most West African coastal systems where it is an important source of protein. Here, we studied its population structure (abundance, biomass, and size) and life history traits (age, annual growth rate, and size for age) under contrasting harvesting conditions at the two largest intertidal systems of the region: Bijagós archipelago in Guinea Bissau (harvested) and Banc d’Arguin in Mauritania (unexploited). To account for local ecological context, we assessed environmental variables that could also affect the abundance and size of Senilia at these sites. We found that the Senilia population of Bijagós is significantly denser, older, with lower standing biomass and smaller-sized shells than the one from Banc d’Arguin. In the Bijagós, the annual growth is a threefold lower and the size for age is half of that at Banc d’Arguin. At both sites, Senilia densities and sizes were correlated with habitat quality indicators: mangrove and mudflat productivity at Bijagós and seagrass and sediment characteristics at Banc d’Arguin. The smaller-sized mature individuals, denser populations, and lower standing biomass at Bijagós compared to Banc d’Arguin are indications of a considerable size-selection pressure at Bijagós.