The seasonal dynamics of the mollusc fauna associated with intertidal eelgrass Zostera noltei beds on the south-eastern coasts of Tunisia (Central Mediterranean Sea) was studied in relation to water column parameters (temperature, salinity and chlorophyll a), sediment type (grain size, percentage of organic matter) and eelgrass bed descriptors (shoot density, leaf height and width, number of leaves per shoot) at two sites in the Gulf of Gabès. From July 2013 to April 2014, samples were collected (five replicates per season and per site) from bare sediments and eelgrass bed. The 4,886 individuals identified belonged to 82 mollusc species from 42 families. Infaunal bivalves such as Scrobicularia plana, Loripes orbiculatus and Macomangulus tenuis were predominant, while the gastropods Jujubinus striatus, Pirenella conica and Bittium reticulatum dominate in the epifauna. Infaunal and epifaunal abundances were positively correlated with leaf biomass and sediment organic matter content, respectively. Species richness and abundance showed significant seasonal variations, with maxima in spring and summer and minima in autumn and winter, and were positively correlated with phenological changes, temperature, and salinity. Our results support that seasonal dynamics of the mollusc assemblage are mainly linked with the biological cycle (e.g., recruitment events) of certain dominant species.