We collected modern diatom samples from two mangrove environments of Sulawesi, Indonesia to provide a much needed dataset for the reconstruction of sea level from tropical environments. The diatom assemblages are dominated by mesohalobous species (e.g.Amphora coffeaeformis, Amphora turgida, Achnanthes delicatula, Nitzschia sigma andTryblionella balatonis) and oligohalobous (e.g. Amphora veneta, Diploneis ovalis andProgonoia didiomatia) taxa. Both study sites show strong vertical zonations, which suggests that duration and frequency of intertidal exposure are important factors in controlling the relative abundance of diatoms. The assemblages can be generally divided into a mixed assemblage of mesohalobous, oligohalobous–halophilous and oligohalobous-indifferent diatoms that are found from the dense mangrove vegetation towards the landward edge of the transects, and mesohalobous diatom assemblages that are located within the fringingRhizophora and tidal flat environments. We subsequently developed a diatom-based transfer function, which is a quantitative approach to sea-level reconstruction. The relationship between observed and diatom-predicted elevations suggests accurate and precise reconstructions are possible. The error estimate (± 0.15 m) is comparable to diatom-based transfer functions from temperate marshes.