Seasonal distribution of dinoflagellate cysts were studied at five surface sediment study stations in Ghar El Melh Lagoon (GML) (Tunisia) in relation to physicochemical parameters and phytoplankton abundance in the water column. At least sixteen dinocyst types were identified, dominated mainly by Protoperidinium spp., Scrippsiella trochoidea complex, Lingulodinum machaerophorum, Alexandrium spp. and Gymnodinium spp., along with many round brown cysts. Cyst abundance ranged from 0 to 229 g−1 dry sediment. No significant differences in cyst distribution were found among stations, though a significant variation was observed among seasons with cyst dominance in autumn. No significant variation was found between cyst abundance and the different abiotic factors monitored, neither in the water column (physicochemical parameters) nor in the sediment (% H2O). Low dinocyst abundance was consistent with the dominance of non-cyst-forming dinoflagellates in the GML water column.