This study investigates pre-colonial and colonial-era pearl fisheries in Sri Lanka using archaeological data from the Gulf of Mannar (GoM). Following surface surveys, test pits were excavated in three pearl oyster middens and one coastal settlement. The archaeomalacological study of the molluscan remains from the middens confirms that the pearl oyster (Pinctada fucata) was the predominant species exploited, providing a clear picture of the pearl oyster bank ecosystems used at the industrial level. Morphometric analysis of the pearl oysters allows for an assessment of exploitation pressure. Ceramic and radiocarbon analyses date the high impact of the pearl industry from the tenth to the nineteenth centuries. The study of by-catch fauna provides insight into pearl bank ecosystems over time. These archaeological findings highlight the impact of industrial extractions on a single species.