Microphytobenthos communities of different sediment types were investigated in intertidal flats of the coastal area around La Rochelle (Pertuis Charentais, France) in July 2014 and January 2015. Biotic variables of biomass, abundance and species composition of microphytobenthos were evaluated together with environmental variables, including irradiance, sediment temperature, grains size, pore water salinity, pH, nutrients, organic matter, water content and heavy metal concentrations in the sediment. The relationships between biotic and environmental parameters showed that: (1) the microphytobenthos biomass and community structures showed significant differences among different sediment types; (2) variation in the microphytobenthos communities were significantly correlated with environmental variables, especially with the heavy metals, grain size, irradiance, pore water salinity, organic matter and concentration of PO4 3+ and Si(OH)4; (3) the species number and richness were both significantly correlated with organic matter, and (4) the species Entomoneis corrugate, Navicula aitchelbee and Gyrosigma cf.limosum were positively correlated to heavy metals, and so were N. phylleptosoma, Surirella brebissonii to Si(OH)4 and NH4 + concentrations, and G. acuminatum and S. brebissonii to PO4 3+ and NH4 +. It is suggested that the spatial variation in biodiversity of microphytobenthos may reflect environmental quality status in coastal intertidal ecosystems.