The Piraquê-Açu and Piraquê-Mirim estuarine system (PAPMES) is located next to the Aracruz City (19˚ 57' S and 40˚ 9' W), Espírito Santo State, Brazil. Palynological analyses were conducted based on two sediment cores (PA20 and PM1). The main purpose of the present study was to recognize and interpret the vegetation dynamics in the region around the collection site in the last 2000 cal yrs BP. The sediment cores were subsampled at each 10 cm depth. The samples were submitted to standard palynological processes. The PA20 sediment core obtained the oldest age of 1758±68 cal yrs BP at a depth of approximately 105-cm. However, the PM1 sediment core obtained the oldest age of ≈2071±82 cal yrs BP at a depth of 95-cm. The comparative record of the sediment cores demonstrated that palynomorphs deposition were directly influenced by local water circulation. Pollen analysis indicated the striking presence of mangrove vegetation, which is mainly characterised by the Rhizophora pollen type. The other vegetation communities underwent little variation over the studied period. The top sediment layers of both sediment cores are characterized by the presence of exotic pollen grains of Eucalyptus, introduced by humans, and by the decrease of the original vegetation.