We collected modern foraminiferal samples to characterize the foraminiferal environments and investigate the role that temporal and spatial variability may play in controlling the nature and significance of foraminiferal assemblages of the mangroves of Kaledupa, Wakatobi Marine National Park, Southeast Sulawesi, Indonesia. The study of foraminiferal live and dead assemblages indicates that dead assemblages are least prone to vary in time and space, and furthermore, they accurately represent the subsurface assemblages that are the focus of paleoenvironmental reconstructions. Further analyses of the dead assemblages indicate a vertical zonation of foraminifera within the intertidal zone. Zone D-Ia is dominated by agglutinated foraminifera Arenoparrella mexicana, Miliammina fusca, M. obliqua and Trochammina inflata. Zone D-Ib has mixed agglutinated/calcareous assemblages with species such as T. inflata and Ammonia tepida. Zone D-II is dominated by numerous calcareous species including A. tepida, Discorbinella bertheloti, Elphidium advenum and Quinqueloculina spp. Zone D-Ia is found to be the most accurate sea-level indicator and its assemblages are omnipresent world-wide. Zones D-Ib and D-II are subject to both spatial and temporal variations which must be included in any sea-level reconstructions.