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Based on 21 years of phytoplankton and environmental monitoring data from the surface water of coastal southeast Arabian Sea, we demonstrate a shift in phytoplankton community towards higher sample genus richness and diatom abundance during the two decades of observations. Analyses were based on 587 water samples collected between 1990 and 2010 and additionally revealed marked long-term changes in sea surface temperature (SST), sea surface salinity (SSS) and turbidity (Secchi depth). The abundances of dinoflagellate genera were positively correlated to SST, particularly during and after the 1997–1998 El Niño Southern Oscillation event. Several diatom genera increased in abundances with decreasing turbidity around and after 1995–2000, mainly the large celled genera Coscinodiscus spp, Odontella spp and Ditylum spp. In 1996–2000, sample genus richness increased from mean of 8–14, and decreased to 11 thereafter. The increase in sample genus richness was linked to the more frequent presence of most taxa during 1996–2000. Increasing Secchi depth and abundance of frequently encountered large-celled diatoms concurrent with decreasing abundances of Trichodesmium spp might signal the alleviation of the nitrogen limitation in the region, favouring diatoms. [ABSTRACT FROM AUTHOR]