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Coastal morphodynamics and environmental changes have been obviously altered by global warming, sea-level fluctuations, and human activities. Palynological analysis is one of the most important tools for providing information on vegetation, climate, and environmental change, which can be relatively sensitive indicators of human activity during the Holocene. However, Holocene coastal morphodynamics and palynological evidence from the Pearl River Delta and coastal areas has not been sufficiently studied. In this paper, we carry out analyses using detailed grain-size and palynological records of pollen, spores, freshwater algae, and marine dinoflagellate cysts from Borehole QZK13 in the Pearl River Estuary (PRE), southern China. The results show information relating coastal morphodynamics, vegetation evolution, climate changes, and anthropogenic activities during the Holocene based on radiocarbon chronology. In general, the PRE experienced marine transgressive processes; sea-level and the coastline tended to migrate landward between 10,700 and 4250 cal yr BP. Meanwhile, abundant arboreal pollen (mainly Castanopsis , Quercus -evergreen, Oleaceae, and Castanea) and small amounts of non-arboreal pollen (mainly Poaceae, Cyperaceae, and Artemisia) were observed in Borehole QZK13, which suggests that subtropical evergreen broadleaved forests were distributed throughout the PRE and adjacent areas, and relatively warm and moist climatic conditions were present during the early-middle Holocene. After that, there were relatively cool and wet climatic conditions, and marine regressive processes occurred in the PRE during the Late Holocene (ca. 4250–960 cal yr BP) indicated by an abrupt increase in aquatic herbs and Dicranopteris. Moreover, we hypothesize that the Neolithic "cultural fault" in the PRE is likely related to frequent storm surges induced by extreme typhoon events that occurred ca. 3000–2700 yr BP. • Grain size, pollen, spores, freshwater algae and dinoflagellate cysts from the Pearl River Estuary were investigated. • Three major phases shown by palynological results were corresponding to the changes in vegetation and climate. • We hypothesized that the Neolithic "cultural fault" is probably related to the storm surges induced by extreme typhoon events. • Natural vegetation cover has suffered large-scale destruction by ancient humans during the Late Holocene. [ABSTRACT FROM AUTHOR]