Pearl farming lagoons are economically important, yet poorly studied ecosystems in French Polynesia. This paper describes a study conducted in 2016 in Takaroa (Tuamotu Archipelago), an atoll recurrently affected by harmful algal bloom (HAB) events. The objectives were to gain insight into phytoplankton community composition, identify the main bloom-forming species and investigate their potential for toxicity. A mesocosm approach was used to assess the response of phytoplankton communities to 3 nutrient treatments: Conway with Si, Si-depleted f/2 and a commercial N-P fertilizer. In total, 87 morpho-species were described from Takaroa lagoon, with dinoflagellates as the most diverse group. Diatoms (Extubocellulus sp., Cylindrotheca closterium, Nitzschia spp.), dinoflagellates (Gymnodinium spp., Heterocapsa spp.) and flagellates (Cryptomonas sp., Pyraminonas spp.) were among the major bloom-forming species identified. Most markedly, Extubocellulus sp., a diatom never reported from French Polynesia before, was able to bloom even in Si-poor environments. Additionally, in vitro cultures of 12 bloom-forming strains were successfully established and tested for their toxicity. Preliminary results suggest that 9 strains, including dinoflagellates (Prorocentrum lima, Amphidinium spp., Heterocapsa sp.), Pyraminonadales (Pyramimonas sp.) and cryptophytes (Cryptomonas sp.), are the likely producers of cyclic imine neurotoxins and toxins acting on voltage-gated sodium channels. The contribution of these toxins to the mortality events previously reported in Takaroa lagoon is further discussed. Overall, this study highlights the relevance of a mesocosm approach which can be applied to other understudied atolls of French Polynesia recurrently threatened by HABs.