The abundance distribution and species richness of encysted plankton have been investigated in the bottom sediments of the Taranto Marine System (southern Italy) for contributing to the understanding of plankton dynamics in a confined coastal area. This confined area is characterized by four contiguous basins with different degrees of confinement. The investigation was carried out in the fall season with the aim to intercept a period of rich cyst production from the plankton before overwintering. From the analysis of a total of 36 sediment samples, from 12 sample sites, the highest abundance of cysts and species richness were registered in the confined part of the system. A total of 103 cyst morphotypes have been recognized in the whole area, with highest abundances and taxa richness in the most confined stations. These results, suggesting a benthic-pelagic exchange of living matter, more intense in confined environments than in the open sea, highlight the necessity of (i) including the analysis of sediment cyst banks in studies of plankton dynamics, and (ii) to consider the role of confined areas, where the variability of environmental conditions favours a higher planktonic biodiversity in the sediments than in the water column.