This study presents the first high-resolution Holocene records of diversity and assemblages of benthic foraminifera from tropical reef environments in the Indian Ocean. Two 3.2. m and 4.4. m long cores from the lagoon of Rasdhoo Atoll (4°N/73°W) in the central Maldives, were sampled at ~. 250. yr intervals. Core #16 covers most of the Holocene (10.32-0. kyr BP) and was taken in the deep lagoon of the atoll (35. m water depth). Core #19 covers the time span 7.375-0. kyr BP and is from a sublagoon (14. m water depth) on the northern margin of the atoll. In Core #16, an early colonization phase during Holocene sea-level rise is characterized by an Ammonia sp. 1 dominated assemblage until ~. 7. kyr BP. The slowdown of sea-level rise in the Mid Holocene (~. 4. kyr BP) marks the onset of a phase of stable environmental conditions in the deep lagoon with high diversity. A shift toward lower diversity and the dominance of Textularia foliacea has occurred from ~. 4-1. kyr BP, which may be explained with the Intermediate Disturbance Hypothesis. An environmental change at ~. 1.4. kyr has caused a distinct faunal change, the decrease of T. foliacea and an increased recovery in diversity. In Core #19, a significant faunal change at ~. 4.0. kyr BP from an Ammonia sp. 2 dominated fauna to a fauna with Ammonia sp. 1, miliolid taxa and a higher diversity might be related to the formation of a sand spit that separates the sublagoon from the main lagoonal basin. The westward extension of the sand spit during the Late Holocene could have changed the restricted bottom water circulation in the main lagoon and caused longer residence times of water and the build-up of lower oxygen and higher nutrient concentrations. This study underlines the importance of the factor time on diversity and the significance of lagoon circulation and bottom water residence times on assemblages and diversity of benthic foraminifera. © 2013 Elsevier B.V.