The dataset encompasses the relative abundances of two epibenthic foraminifera, namely Cibicides kullenbergi and Cibicides wuellerstorfi, at DSDP Sites 216 (situated on the northern side of the Ninetyeast Ridge) and 217 (located in the northernmost part of the Ninetyeast Ridge), as well as ODP Site 758 (positioned along the crest of the Ninetyeast Ridge, midway between DSDP Sites 216 and 217). These sites are situated in the northeastern equatorial Indian Ocean. The selection of these epibenthic species was motivated by the objective to investigate the impact of tectonic gateways and Antarctic glaciation on deep water masses in the northeastern equatorial Indian Ocean since the early Miocene.