An unusual phytoplankton bloom dominated by unidentified green coloured spherical algal cells (∼5 𝜇 m diameter) and dinoflagellates (Heterocapsa, Scripsiella and Gymnodinium) was encountered along the coast of Goa, India during 27 and 29 January, 2005. Pigment analysis was carried out using both fluorometric and HPLC methods. Seawater samples collected from various depths within the intense bloom area showed high concentrations of Chl 𝑎 (up to 106 mg m−3) associated with low bacterial production (0.31 to 0.52 mg C m−3 h−1) and mesozooplankton biomass (0.03 ml m−3). Pigment analyses of the seawater samples were done using HPLC detected marker pigments corresponding to prasinophytes, dinoflagellates and diatoms. Chlorophyll 𝑏 (36–56%) followed by peridinin (15–30%), prasinoxanthin (11–17%) and fucoxanthin (7–15%) were the major diagnostic pigments while pigments of cryptophytes and cyanobacteria including alloxanthin and zeaxanthin formed > 10%. Although microscopic analysis indicated a decline in the bloom, pheaophytin concentrations in the water column measured by both techniques were very low, presumably due to fast recycling and/or settling rate. The unique composition of the bloom and its probable causes are discussed in this paper.