High abundances of mangrove pollen have been associated with transgressive cycles on tropical margins, but the detailed relations between systems tracts and the taphonomy of the pollen are unclear. We report here the occurrence and high abundance of Rhizophora pollen, in association with taraxerol, a Rhizophora-sourced biomarker, from a high-resolution Congo fan core covering the last deglaciation. An age model based on 14C dates enables the temporal changes in taraxerol content and the percentage frequencies and flux (pollen grains (pg) cm–2 (103 yr)–1) of mangrove pollen to be compared quantitatively with the lateral rate of transgression across the flooding surface (derived from glacio-hydro-isostatic model output and the bathymetry of the margin). Rhizophora pollen concentrations and taraxerol content of the sediment are very strongly positively correlated with the lateral rate of transgression and indicate, independently of any sequence stratigraphic context, that mangrove pollen spikes are associated with the transgressive systems tract rather than the highstand systems tract or maximum flooding surface. Lower-resolution longer-term records from this margin indicate an association between taraxerol concentrations and transgressive rather than regressive phases. The flux of these materials to the Congo fan is interpreted as a function of the erosion of flooded mangrove swamp on the shelf and less importantly, changing extent of mangrove habitat, during sea-level rise. Congo River palaeoflood events also result in reworking of mangrove pollen and supply to the fan, but this mechanism is subdominant. Rhizophora pollen has been underestimated in many palynological studies undertaken on cores from the African margin because of inappropriate sieve mesh size used during laboratory preparation.