We present pollen and stable isotope (δ13C, δ18O, δ15N) data from a ∼4 m core (TNF-1) of primarily mangrove peat taken from Turneffe Atoll, Belize. Radiocarbon (accelerator mass spectrometry) dates show that the record represents ca. 5000 years of sediment accumulation. Vegetation composition varied between dominant mangroves (primarily Rhizophora mangle) and Chenopodiaceae-Amaranthaceae, most likely Salicornia bigelovii. The pollen data, along with inferences from stable isotope analyses of bulk peat and fossil leaf fragments, indicate that marked environmental changes occurred at this location over the past ca. 5000 years. There was a transition between ca. 4100 and 2900 cal yr BP, from vegetation dominated by relatively tall mangroves (R. mangle) to one dominated by Chenopodiaceae-Amaranthaceae and then Myrica, most likely wax myrtle (M. cerifera). These changes bracket a period centered at ca. 3500 calibrated years before present, where there is a peak in the δ18O of mangrove leaf fragments. This timing corresponds with other paleoenvironmental records of climate drying in Central America and increases the geographic and habitat scope (i.e., mangrove habitat) of records documenting these changes. Interpretations of shifts in mangrove habitat, however, require consideration of additional environmental influences, including changes in groundwater hydrology and relative inputs of seawater and freshwater (i.e., precipitation) during the Holocene.