Abundant phytoplankton and bacteria were identified by microscopy and high-throughput 16S rRNA tag Illumina sequencing of samples from water- and ice phases collected during winter at two central European Great Lakes, Balaton and Fertő (Neusiedlersee). Bacterial reads at all sites were dominated (>85%) by Bacteroidetes and Proteobacteria. Amongst phototrophs, microscopy and 16S sequencing revealed that both phytoplankton and cyanobacteria were represented, with a median of 1500 cyanobacterial sequence reads amongst 13 samples analyzed. The sequence analysis compared replicate Balaton and Fertő ice and water samples with an outgroup from three Hungarian soda lakes. In particular, both water and ice from Fertő contained high contributions from cyanobacteria. Two percent of total reads identified to the level of family in water at Fertő were dominated by a single operational taxonomic unit (OTU) of a cyanobacterium within the Rivulariaceae, which was largely absent from ice. Conversely, ice samples from both lakes yielded an abundant OTU assigned to a Flavobacterium sp. known to be associated with freshwater ice. Principal Coordinates Analysis (PCoA) revealed that the ice communities from all sites were similar to one another, and that the water communities did not cluster together. Fluorescence emission spectra obtained at 77 K confirmed the presence of intact cyanobacteria in Fertő water and ice. Photosynthetic characterization of phototrophs resident in water and ice analyzed by assay of acid-stable photosynthetic H¹⁴CO₃^– incorporation showed that communities from both phases were photosynthetically active, thus adding to growing recognition of ice-covered lakes as viable habitat for phototrophs.