Sediment, pollen and charcoal data, set within a radiocarbon chronological framework, from Unguja Ukuu, Zanzibar are used to reconstruct mangrove ecosystem dynamics during the Holocene. Changes in mangrove ecosystem composition were driven by a combination of sea level and environmental changes, anthropogenic interaction and geomorphological activity. The high occurrence of Rhizophora mucronata, accompanied by other mangrove species, suggests that the headland of Unguja Ukuu supported a mangrove community from about 7000 cal BP. During the mid-Holocene, mangroves migrated landward, probably in response to a sea level highstand. After the mid-Holocene a short term decrease in Sonneratia alba, with an increase in more terrestrial mangrove species, the appearance of Poaceae and increase in the quantity of charcoal all indicate a lower sea level and relatively dry environmental conditions. This is likely to be coincident with the appearance of the earliest habitation of Zanzibar. The increase in S. alba pollen until prior to 530cal BP is likely to reflect a sea level rise. The increase in charcoal after about 1400 cal BP is likely to relate to drier conditions and may reflect early human settlement at Unguja Ukuu. A recent decrease in R. mucronata, combined with an increase in S. alba, is likely to result from sea level rise and decreased moisture availability. Recent human-ecosystem interactions are characterized by a reduction in mangrove extent, possibly associated with the mangrove pole trade and rising fuel wood consumption in Zanzibar, particularly from around 530 cal BP.