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Kongsfjorden is a small Arctic fjord but with great hydrographic complexity and has changed greatly due to the climate change. Arctic warming has increased melts of sea ice and glaciers that results in higher freshwater content. Microbial community variability and increasing terrestrial input were detected continuously in recent years ITag eukaryotic 18S rRNA V4 metabarcoding, photosynthetic pigments analysis and epifluorescence microscopy were used to reveal the dominant species of small eukaryotic community (<20 μm). Both Spearman correlation and redundant analysis were used to study the correlation between the small eukaryotes and the environmental conditions. In the present study, the surface water with salinity lower than 34 was thicker than in summers of previous years. The freshwater mixotrophic chrysophyte Poterioochromonas malhamensis was found for the first time as the dominant species. No general trends were found for the contributions of P. malhamensis to the total reads of small eukaryotes in water depths; and no obvious differences were found at different stations and water masses. Phagotrophy, which is more common than phototrophy at all times in P. malhamensis, is thought to be the main reason for the prevalence of P. malhamensis in Kongsfjorden. The occurrence of P. malhamensis induced a disorder in the small eukaryotic community, which biodiversity and composition showed weak correlation with the water masses. The dominance of the freshwater-originating phytoplankton may indicate an ecosystem change in the Kongsjforden, which probably might become more remarkable in the future as the climate continues to change. [ABSTRACT FROM AUTHOR]