We investigated the distribution of modern benthic foraminifera from Kelantan waters in the western part of the Sunda Shelf, South China Sea. Twenty-nine benthic foraminiferal species were identified from seven samples collected along a ∼250 km-long transect perpendicular to the Kelantan coastline. Calcareous hyaline species made up 57% of the overall assemblages collected in the study area, followed by calcareous porcelaneous (23%) and agglutinated (20%) species. Cluster analysis recognised two distinctive groups. Group A represented the shallow inner-shelf area (19–35 m water depth) with a coarse sand-dominated substrate where Amphistegina papillosa (13.37%) and Assilina ammonoides (11.04%) were highly abundant. Group A had lowest diversity with no agglutinated species. Group B, occurred at 40–60 m water depth, had higher foraminiferal diversity and was characterised by a very fine sand substrate. The foraminiferal assemblages here were dominated by calcareous hyaline species in group B followed by calcareous porcelaneous and agglutinated species. Group B was characterised by Assilina ammoinodes (11.04%), Heterolepa dutemplei (10.29%), and Discorbinella bertheloti (10.03%). The dominant agglutinated species in Group B were Textularia agglutinans (4.93%) and Cylindroclavulina bradyi (3.55%). Shallow-water species, such as Amphistegina spp., were absent from Group B. Our study shows that the distribution of benthic foraminiferal assemblages from the western Sunda shelf off Kelantan, is closely associated with changes in seafloor sediment, distance from the shore, and water depth.