Within the framework of research aimed at using genetic methods to evaluate harmful species distribution and their impact on coastal ecosystems, a portion of the ITS1rDNA of Alexandrium minutum was amplified by real-time PCR from DNA extracts of superficial (1–3 cm) sediments of 30 subtidal and intertidal stations of the Bay of Brest (Brittany, France), during the winters of 2013 and 2015. Cell germinations and rDNA amplifications of A. minutum were obtained for sediments of all sampled stations, demonstrating that the whole bay is currently contaminated by this toxic species. Coherent estimations of ITS1rDNA copy numbers were obtained for the two sampling cruises, supporting the hypothesis of regular accumulation of A. minutum resting stages in the south-eastern, more confined embayments of the study area, where fine-muddy sediments are also more abundant. Higher ITS1rDNA copy numbers were detected in sediments of areas where blooms have been seasonally detected since 2012. This result suggests that specific genetic material estimations in superficial sediments of the bay may be a proxy of the cyst banks of A. minutum. The simulation of particle trajectory analyses by a Lagrangian physical model showed that blooms occurring in the south-eastern part of the bay are disconnected from those of the north-eastern zone. The heterogeneous distribution of A. minutum inferred from both water and sediment suggests the existence of potential barriers for the dispersal of this species in the Bay of Brest and encourages finer analyses at the population level for this species within semi-enclosed coastal ecosystems.