The mangrove ecosystem is one of the most distinctive biospheres, and it is under threat from habitat loss, aquaculture expansion, overharvesting, and pollution, all of which impact the malacofaunal diversity. This study aimed to investigate the malacofaunal diversity along the mangrove region of the Gulf of Mannar (GoM) and Physico-chemical properties of the sediments were measured to correlate the malacofaunal diversity. The diversity of the molluscs along the Thoothukudi coast was investigated from December 2020 to September 2021, documenting 84 mollusc species, represented by 45 gastropods and 39 bivalves. The class Gastropoda represented 7 orders, 15 families, and 30 genera, with Caenogastropoda having the highest species (19), followed by Neogastropoda with 7 species, while in bivalves, Venerida had the most species (14 species), followed by Cardiida (9 species). Palayakayal had the greatest number of species (68), followed by Punnakayal (63), Karapad Bay (32), and Machoda Bridge (33). Palayakayal has the highest Shannon–Wiener diversity index (H’) and Margalef species richness (d) at 4.11 and 10.81, followed by Punnakayal at 4.05 and 10.16; Karapad at 3.39 and 5.65; and Machoda Bridge at 3.55 and 3.55 respectively. The BC (Bray–Curtis) similarity index identified the most similarity (86.91%) between Palayakayal and Punnakayal. Palayakayal has the greatest (H’) and (d) values due to its pristine mangrove habitat and low anthropogenic activity. The Physico-chemical results showed that salinity and diversity were positively correlated, while hydrogen sulfide, organic matter, and molluscan diversity were negatively correlated. The malacofaunal diversity has been documented to provide useful baseline data for conservation management. Additionally, the findings showed that salinity is a crucial factor in favoring diversity. The anthropogenic activities in the ecosystem first alter the salinity of the soil, directly impacting malacofaunal diversity. Such studies might increase knowledge among the public and policy-makers, enabling them to develop legislation adequately.