The Spratly Islands are located in a vast area with numerous coral reefs in the South China Sea within the highly biodiverse Indo-Pacific region. Benthic foraminifera were investigated from two unstudied, remote atolls: Louisa Reef (LR) and Royal Charlotte Reef (RC). These atolls are about 250 kilometers off Brunei Darussalam, situated at the northern coastline of Borneo. We compare diversity and distribution of the benthic foraminifera from these atolls with those reported from shallow water setting in Brunei. Environmental conditions nearshore Brunei is very different due to strong influence of riverine runoff resulting in eutrophic and siliciclastic conditions, whereas the atolls are oligotrophic, and carbonate dominated. The composition and diversity of larger benthic foraminifera (LBF) clearly reflects such environmental differences. The most common species of LBF in the atolls are Calcarina defrancei, C. hispida, Amphistegina lobifera, A. radiata, Amphisorus hemprichii, and Parasorites orbitolitoides. The smaller benthic foraminifera are less abundant and much less species were recovered, still there are common taxa such as Tretomphaloides concinnus and Textularia agglutinans. The soritids, are common in the carbonate atolls, but are very rare in the nearshore Brunei: in fact, only the species Amphisorus hemprichii was found in two shallow reefs so far (Telesai and Hornet reefs, western part of Brunei coast). The results obtained also indicate that the dominant LBF species found in the atolls show different depth distribution with respect to the nearshore species. Despite the two atolls are characterized by comparable environmental conditions and are 70 kilometers apart, data show several differences in the benthic foraminifera community structure. By comparing data from the two atolls and the nearshore Brunei fauna, we can draw attention to the questions of LBF migration patterns and strategies that are here discussed: the interpretation points to a species-specific adaptation capacity probably resulting from different colonization events over time.