Oceanic waters of the Northern Arabian Sea experience massive algal blooms during winter–spring (mid Feb–end Mar), which prevail for at least for 3 months covering the entire northern half of the basin from east to west. Ship cruises were conducted during winter–spring of 2001–2012 covering different stages of the bloom to study the biogeochemistry of the region. Phytoplankton analysis indicated the presence of green tides of dinoflagellate, Noctiluca scintillans (=N. miliaris), in the oceanic waters. Our observations indicated that diatoms are coupled and often co-exist with N. scintillans, making it a mixed-species ecosystem. In this paper, we describe an approach for detection of bloom-forming algae N. scintillans and its discrimination from diatoms using Moderate Resolution Imaging Spectroradiometer (MODIS)-Aqua data in a mixedspecies environment. In situ remote sensing reflectance spectra were generated using Satlantic™ hyperspectral radiometer for the bloom and non-bloom waters. Spectral shapes of the reflectance spectra for different water types were distinct, and the same were used for species identification. Scatter of points representing different phytoplankton classes on a derivative plot revealed four diverse clusters, viz. N. scintillans, diatoms, non-bloom oceanic, and non-bloom coastal waters. The criteria developed for species discrimination were implemented onMODIS data and validated using inputs from a recent ship cruise conducted in March 2013.