The marine benthic diversity of the Palawan/North Borneo ecoregion is poorly known, despite its implied unique high species richness within the Coral Triangle. The present study investigated the diversity and distribution of benthic foraminifera on the Brunei shelf. The objectives were to determine the species composition of sediment samples collected from 11 sites, extending ~70 km from the Brunei coastline and along a depth gradient of 10–200 m. We retrieved a total of 99 species, belonging to 31 families and 56 genera, out of which 52 species represented new records for Brunei and probably the ecoregion. Using presence/absence data, analyses were also performed to compare species diversity patterns (species richness, occupancy, taxonomic distinctness) and species assemblage similarity across the sites. For further insight into the relationship between distribution and depth-associated environmental conditions, we undertook stable isotope analyses of selected species of Rotaliida, Miliolida, and Lagenida. Oxygen isotope values were positively correlated with depth and species distribution, confirming cooler temperatures at greater depth. The carbon isotope data revealed species differences relating to habitat and food source specificity and a biomineralization effect. Close to one-third of the species were recorded from single sites, and species richness and taxonomic distinctness increased with depth and were greatest at the second deepest site (144 m). Together, these findings suggest data underrepresentation of diversity, habitat disturbance in shallower water, and species specialization (adaptation) in deeper water. Importantly, assemblage similarity suggests the occurrence of at least three marine biotopes on the Brunei shelf (10–40 m, 40–150 m, and >150 m). This study contributes significantly to our understanding of the local and regional patterns of foraminiferal diversity and distribution.