Phytoplankton research of the Danube River at 1388 r. km (Croatian section, the area of Kopački Rit Nature Park) was performed at monthly intervals during the period January-October 2012. A total number of 170 phytoplankton taxa were detected, indicating the high biodiversity of the phytoplankton in the Danube River. Throughout the studied period, diatoms (species from group Bacillariophyceae) had the highest abundance, contribution to total qualitative composition and total biomass of phytoplankton. In addition to the planktonic diatom species, benthic diatoms that were raised from benthos during the water turbulence, were also detected. According to the phytoplankton functional group classification, identified species were sorted into 22 functional groups. During the whole studied period, the most representative were diatoms from the group TB and D, with the highest abundance and contribution to total biomass of species Stephanodiscus hantzschii and Cyclotella meneghiniana. In addition to diatom community, species from group C, MP and P appeared occasionally. Expected development of green algae and cyanobacteria was not detected. Given results present the basis for ecological status evaluation of the Danube River at the studied section.