Phytoplankton is responsible for most primary production in Antarctica, but the short timescale dynamics of its size structure and composition are poorly described and understood. The abundance and composition of phytoplankton in Fildes Bay, western Antarctic Peninsula, was followed for 12 days during the summer using a range of methods, including size fractionation of chlorophyll, microscopy, flow cytometry and terminal-restriction fragment length polymorphism (T-RFLP) of the plastid 16S rRNA gene. A rapid increase in biomass and cell abundance occurred in response to a vertical mixing event. This increase also resulted in a shift in composition from diatoms to Prymnesiophyceae, and then back to diatoms as the water column re-stratified. Our results show a strong dominance of nanophytoplankton represented by Thalassiosira and Phaeocystis. The rapid response of the phytoplankton suggests that it is well adapted to short-term environmental changes.