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We analysed the BSi (Biogenic Silica) contents of the marine core SK-313/1 from the southeastern Arabian Sea which is dated up to ~14.5 kyr BP. Results show that the maximum and minimum BSi contents are 2.5 and 0.5%, respectively. This is because of the low supply of silica skeleton and the high dissolution and dilution of terrigenous materials. The BSi mass accumulation rates indicate a trend of reduced paleoproductivity during the late Glacial period and increase during the Holocene, with global climatic shifts. Insolation changes at low latitudes, which regulate temperatures, may affect nutrient availability and, consequently productivity variations on a glacial–interglacial timescale. Notably, millennial events like the Younger Dryas (YD) periods, exhibited lower paleoproductivity, in contrast to the Bølling/Allerød (B-A) period and the middle Holocene, which displayed elevated levels of paleoproductivity. These millennial-scale fluctuations in siliceous productivity may be due to the changes in nutrient supply caused by the Indian summer monsoon (ISM). The period of increased paleoproductivity could be influenced by intensified chemical weathering and a boosted nutrient supply, which are consequences of the strengthened ISM during periods of relatively higher temperature.