AbstractGlacial melt has a great influence on biological communities of the Antarctic Peninsula. Annual changes in heterotrophic flagellates from March 2008–March 2009 and effects of glacial melting on heterotrophic flagellates from December 2008–March 2009 were studied within the coastal zone of King George Island. The maximum abundance and biomass occurred in November and December (950.6–1236.2 individuals ml^-1; 0.02–0.035 μg C ml^-1), and the minimum in May and June (419.8–456.8 individuals ml^-1; 0.018–0.019 μg C ml^-1). Forty-five species were identified. The diversity of choanoflagellates, euglenids, bicosoecids, kinetoplastids and incertae sedis flagellates was greatest. Glacial melt between December and April resulted in the freshening of the surface water at the Collins Bay, giving rise to a vertical gradient of salinity (from 26‰ at the surface to 34‰ at the near-bottom layer). The trophic, size and species structure of the heterotrophic flagellates was simplified due to freshening of the surface waters. Eurybiontic and cosmopolitan species were significantly enriched in the freshened surface layer, with prevalence of small-sized mobile bacterio-detritovorous forms. The simplification of structure of the assemblage of heterotrophic flagellates can affect the stability of biological communities.