Late Paleocene and Early Eocene climates and ecosystems underwent significant change during several transient global warming phases, associated with rapidly increasing atmospheric carbon concentrations, of which the Paleocene-Eocene Thermal Maximum (PETM; approximately 55.5 Ma) is best studied. While biotic response to the PETM as a whole ( approximately 170 kyrs) has been relatively well documented, variations during the PETM have been neglected. Here we present organic dinoflagellate cyst (dinocyst) distribution patterns across two stratigraphically expanded PETM sections from the New Jersey Shelf, Bass River and Wilson Lake. Many previously studied sites show a uniform abundance of the thermophilic and presumably heterotrophic taxon Apectodinium that spans the entire carbon isotope excursion (CIE) of the PETM. In contrast, the New Jersey sections show large variations in abundances of many taxa during the PETM, including the new species Florentinia reichartii that we formally propose. We infer paleoecological preferences of taxa that show temporal abundance peaks, both qualitative and absolute quantitative, from empirical as well as statistical information, i.e., principle (PCA) and canonical correspondence analyses (CCA). In the CCAs, we combine the dinocyst data with previously published environmental proxy data from these locations, such as TEX (sub 86) paleothermometry, magnetic susceptibility and sedimentary size fraction. The combined information supports previous inferences that sea level rose during the PETM, but also indicates a (regional) increase in fresh-water runoff that started approximately 10 kyr after the onset of the CIE, and perhaps precession-paced cycles in sea surface productivity. The highly variable dinocyst assemblages of the PETM contrast with rather stable Upper Paleocene assemblages, which suggests that carbon input caused a dynamic climate state, at least regionally.