Dinoflagellate cyst assemblages from 15 modern surface sediment samples of the Bay of Quiberon (Southern Brittany shelf) have been examined to assess their potential as marine bio-indicators for paleoenvironmental reconstructions in a shallow coastal environment. Some discrepancies are noted in the distribution of dinocyst taxa in the study area, and particularly regarding dinocyst concentration and diversity (26 different taxa identified in total) as well as heterotrophic taxa percentages. We suggest that the proportion of heterotrophic taxa is, in an embayment of 15 m deep in average, mainly attributed to bottom water oxygenation and sediment granulometry, both acting on species-selective degradation after dinocyst deposition. More precisely, higher heterotrophic abundances are found under lower oxic conditions and in fine grain-size sediment samples, leading to caution about their use as productivity indicators in coastal environments when these parameters are not fully addressed. The comparison of the Bay of Quiberon data with surface sediment samples and top cores from previously published data makes it possible to establish a transect of the modern dinocyst distribution from inshore to offshore areas in the northern Bay of Biscay, allowing to identify different ecological groups according to the hydrological and bathymetric contexts: i) an estuarine assemblage strongly dominated by Lingulodinium machaerophorum, ii) a proximal coastal assemblage dominated by L. machaerophorum and, to a lesser extent, Spiniferites bentorii, iii) a neritic assemblage dominated by L. machaerophorum, Spiniferites ramosus and cysts of Pentapharsodinium dalei, and iv) an oceanic group dominated by Spiniferites mirabilis and Operculodinium centrocarpum.