Southeastern Australia's marine waters are notably warming, surpassing global averages. This region has emerged as a strategic location for researching planktic microfossils, particularly dinoflagellate cysts, in modern and Late Quaternary sediments, offering crucial insights into the biophysical properties of mid-latitude waters. This study examined cyst distribution in marine sediment cores near Maria Island, Tasmania, southeastern Australia, up to 9000 years before present (kyrs BP). Dominant cysts included Protoceratium reticulatum, Protoperidinium spp. (P. avellana, P. conicum, P. oblongum, P. subinerme, P. shanghaiense), and Spiniferites spp. (S. bulloideus, S. hyperacanthus, S. membranaceus, S. mirabilis, S. pachydermus, and S. ramosus). Inshore, Spiniferites spp. constituted a higher proportion (up to 61%), while offshore was dominated by P. reticulatum (up to 80%). Impagidinium spp. and Nematosphaeropsis labyrinthus were exclusively found offshore and displayed increased abundance from ∼6 kyrs BP, suggesting a shift from a shallow to a deep-water habitat. Alexandrium tamarense species complex cysts were present over 140 years inshore and approaching 9 kyrs BP offshore, indicating a longstanding endemic presence. Gymnodinium catenatum cysts were detected exclusively inshore from ∼50 years ago, indicating a relatively recent bloom phenomenon. The East Australian Current's limited southward reach is suggested by the absence of the warm-water cyst-producing taxon Lingulodinium polyedra. Similarly, the non-detection of the cold-water species Spiniferites antarctica and Impagidinium pallidum reflects Subtropical Front boundaries against subantarctic incursions from the south. In contrast to coccolithophores in the same core, no noticeable shift from cold to warm-water dinoflagellate cyst species was observed. This documentation of dinoflagellate cysts aids in predicting environmental impacts on local communities and beyond.