The Beagle Channel is a remote subantarctic environment where mussel aquaculture initiatives have existed since the early 1990s. Here we analyze phytoplankton biomass and composition, and the occurrence of harmful microalgae species and their toxins at three sites during the period 2015–2016. The occurrence of potentially harmful algae was observed throughout the study period, including toxigenic dinoflagellates such as Alexandrium catenella (Group I of the A. tamarense complex), A. ostenfeldii, Dinophysis acuminata, Gonyaulax spinifera, Azadinium sp., and the diatoms Pseudo-nitzschia australis and P. fraudulenta. Toxic dinoflagellates were detected in low densities whereas a Pseudo-nitzschia bloom was observed in late February. Isolates of A. catenella and P. delicatissima sensu stricto were phylogenetically characterized. The toxin profile of A. catenella was dominated by GTX4, while P. delicatissima sensu stricto showed no production of the neurotoxin domoic acid in culture conditions. The results provide base-line information for the management of harmful algal blooms in this little explored subantarctic area.