Phytoflagellates < 10 μm substantially contribute to the abundance, biomass and primary production in polar waters, but information on the distribution of specific groups is scarce. We applied catalysed reporter deposition‐fluorescence in situ hybridization to investigate the distribution of total phytoflagellates and of eight specific groups along a 100 km transect west off Kongsfjorden (Spitsbergen) from 29 to 31 July 2010. Phytoflagellates contributed to > 75% of the depth‐integrated abundance and biomass of total eukaryotes < 10 μm at all stations. Their depth‐integrated abundance and biomass decreased along the transect from 1.5 × 10¹² cells m⁻² (6.6 × 10¹² pgC m⁻²) at the outermost station to 1.7 × 10¹⁰ cells m⁻² (4.7 × 10¹⁰ pgC m⁻²) at the innermost station. Chlorophytes contributed to the total abundance of phytoflagellates with a range from 13% to 87% (0.7–30.5 × 10³ cells ml⁻¹), and predominated in open waters. The contribution of haptophytes was < 1–38% (10–4500 cells ml⁻¹). The other groups represented < 10%. The temperature and salinity positively correlated with the total abundance of phytoflagellates, chlorophytes, haptophytes, bolidophytes and pelagophytes. Cryptophytes, pedinellids and pavlovophytes were negatively associated with the nutrient concentrations. The community composition of phytoflagellates changed along the transect, which could have implications on food web dynamics and biogeochemical cycles between the open ocean environment and Kongsfjorden investigated here.