Rogoznica Lake (Croatia) is a typical example of marine meromictic lake. Holomictic events are rare and happen after long periods of stratification durin which oxygen consumption results in occurrence of anoxic holomictic conditions in the whole water column. fast intrusion of the nutrient rich bottom waters to the surface decreases the N/P ratio because of P release from the bottom waters. In contrast, there is P limitation in the surface water during spring and summer stratification. During and after the appearance of anoxic holomixis, the whole water column appears as N limited. This highly influences biology of the lake. However, little is known about prokaryotic communities under these conditions. Therefore, the aim of this study was to determine the community structructure and the abundance of prokaryotic organisms by quantitative PCR and high-throughput 16S rRNA gene sequencing of DNA.