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Nitrogen isotope analysis of chloropigments provides information on the sources of nitrogenous nutrients assimilated by phytoplankton. The abundant, ubiquitous chlorophyll a records nitrogen isotopic compositions (δ15N) of eukaryotic phytoplankton and cyanobacteria, whereas more source‐specific chloropigments, such as the divinylchlorophylls exclusively possessed by the marine picocyanobacterium Prochlorococcus, can potentially resolve isotopic variability within the phytoplankton community. In this study, we analyzed the δ15N of both chlorophyll a and divinylchlorophyll a isolated from suspended particulate material collected at the subsurface chlorophyll maximum (SCM) along a meridional transect at 88°E in the oligotrophic eastern Indian Ocean. The nitrogen isotopic compositions of Prochlorococcus (δ15NPRO) and the combined biomass of eukaryotic phytoplankton and Synechococcus (δ15NEU+SYN) estimated from the δ15N of divinylchlorophyll a and chlorophyll a, respectively, revealed systematic variations that were not apparent from bulk isotope measurements. Whereas consistently low δ15NPRO indicated reliance of Prochlorococcus on regenerated nitrogen throughout the transect, elevation in δ15NEU+SYN values at several stations was interpreted to reflect assimilation of subsurface NO3− by eukaryotic phytoplankton. The δ15N distributions revealed subtle differences in NO3− availability at the SCM along the transect, which were consistently explained by the occurrence of mesoscale eddies in the Bay of Bengal, deepening of the mixed layer induced by a seasonal Wyrtki Jet in the equatorial region, and substantial deepening of the nutricline in the South Indian Ocean gyre. Our results highlight the utility of compound‐specific isotopic measurements of multiple species of chlorophylls in obtaining essential non‐incubation‐based biogeochemical constraints on the primary production in the ocean. Key Points: We determined nitrogen sources for phytoplankton based on nitrogen isotopic measurements of chlorophyll a and divinylchlorophyll aProchlorococcus depended on regenerated nitrogen whereas eukaryotic phytoplankton responded sensitively to the subsurface nitrate supplyPhytoplankton responses were consistently explained by oceanographic conditions along a meridional transect in the eastern Indian Ocean [ABSTRACT FROM AUTHOR]