This paper is a report on the diatoms and dinoflagellate cysts identified in a sediment core and a water sample recovered from Rookery Bay, a subtropical estuarine system located on the west coast of Florida. Eighty-eight diatom taxa representing 48 genera, many of which have been rarely observed, and 14 dinoflagellate cyst genera with 20 taxa were identified in Rookery Bay. All taxa are briefly annotated and documented by light micrographs. The most common diatom taxa in the surface sediment sample are Amphicocconeis disculoides, Chaetoceros resting spores, Cyclotella litoralis, Cymatosira belgica, Neodelphineis pelagica, Paralia sulcata, and Pleurosigma rhombeum. The most abundant dinoflagellate cyst taxa in the surface sample include Brigantedinium spp., Lingulodinium machaerophorum, Polyspheridium zoharyi, Spiniferites bentorii, and Spiniferites ramosus.