The spatiotemporal distribution of phytoplankton within Tanzanian coastal waters, and within Pemba Channel in particular, is considered to be poorly known. Improved knowledge of the phytoplankton community, including the spatiotemporal distribution, is desirable for understanding certain aspects of trophic linkages to small pelagic fish, a key marine resource in Tanzania, and for understanding how anthropogenic activities such as terrestrial run-off and effluent discharge may impact the phytoplankton community of these waters. In this study the abundance, diversity and distribution of microphytoplankton was determined throughout the Pemba Channel during the Southeast monsoon and assessed in relation to local environmental parameters. A total of 88 species were identified during this study. Generally, diatoms dominated the microphytoplankton community of the Pemba Channel with 55 identified species (62.5% of total), followed by 31 dinoflagellate species (35.2%) and 2 cyanobacteria species (2.27%). Abundances were low, generally less than 100 cell L-1. Despite a clear dominance by diatoms within the samples, no obvious spatial pattern in their distribution was identified within the channel. Cyanobacteria meanwhile displayed a significant latitudinal gradient being more abundant in the northern half of the channel. Several harmful or potentially harmful phytoplankton species were also identified in this study including Pseudo-nitzschia sp. and Dinophysis sp., although their abundances were below the thresholds of harmful algal bloom warning systems. Nevertheless, to understand whether these species are increasing with time in response to anthropogenic activities, thus having the potential to become problematic in future, regular phytoplankton monitoring programs are recommended.