This dataset contains genus-level counts (#) of benthic foraminifera identified from the 125–2000 µm fraction of 51 inter-reef seafloor surface sediment samples from the Spermonde Archipelago, SW Sulawesi, Indonesia. A total of 42 genera are reported, spanning three ecological groups: symbiont-bearing larger benthic foraminifera (including Amphistegina, Operculina, Planoperculina, Heterostegina, Nummulites, Peneroplis, Alveolinella, Borelis, Dendritina, Sorites, Parasorites, Calcarina, and Baculogypsina); small heterotrophic taxa (including Cibicides, Cibicidoides, Quinqueloculina, Triloculina, Pyrgo, Spiroloculina, Cancris, and others); and stress-tolerant taxa indicative of elevated nutrient or turbidity conditions (including Nonion, Ammonia, Elphidium, Textularia, Reusella, and others). Counting methodology follows the FoRAM Index protocol (Hallock et al., 2003) with adjustments for non-reef settings (Prazeres et al., 2020). These data underpin foraminiferal assemblage analysis, cluster classification, and calculation of the FoRAM Index (FI) as an ecological proxy for photic and trophic conditions across the shelf. The field sampling was performed in August 2021 in the framework of the HAnsea project, sample depths range from 4.5 to 73.6 m water depth. Data collection was done between June 2023 and April 2024.