Our survey has revealed that the phytoplankton in the anthropo-hypersaline lakes of the Transylvanian Basin (Romania) was often dominated by photoautotrophic picoplankton (PPP, cells with a diameter <2 μm). Therefore, the aim of this study was to identify PPP members both in the summer and the winter communities using molecular biological techniques, denaturing gradient gel electrophoresis (DGGE) and sequence analysis. The applied PCR-DGGE methods were highly specific to cyanobacteria and green algae. A total of 11 different plankton taxa were identified that were related to several distant taxonomic groups. PPP were represented by a simple community and consisted of two major genotypes, one from the green algal species Picochlorum oklahomense and the other related to marine Synechococcus isolates (Cyanobacteria). These marine PPP species were recorded for the first time in inland saline lakes from Europe. Besides picoplankton, several additional marine taxa (e.g. cryptophytes and haptophytes) were detected among the nanoplankton species. The presence of the identified marine and hypersaline species could be explained by wind, precipitation or waterfowl transfer; however, this latter could have smaller importance.