Knowledge of the functions, interactions, and diversity of extremely halophilic microorganisms mostly comes from the results of studies performed in different salterns throughout the world. As model habitats, salterns allow the comparison of different techniques used for qualitative and quantitative analysis of halophilic communities in these hypersaline environments. Camalti Saltern is the biggest coastal solar saltern located on the Aegean coast of Turkey, and it produces most of the salt consumed in the country. In the present study, detection of prokaryotic communities of the Camalti Saltern was performed using 2 culture-independent methods. Real-time polymerase chain reaction (RTPCR) and fluorescein in situ hybridization (FISH) techniques were evaluated to analyze the microbial populations of Camalti Saltern. Of the Camalti samples, 48% to 67% were hybridized with the EUB338 probe and 33% to 57% were hybridized with the ARC915 probe. Repeatability of the RT-PCR experiments with environmental DNA was considered insufficient. However, FISH analysis may be combined with RT-PCR and these 2 techniques may be used in tandem to rapidly reveal quantitative aspects of the microbial population of hypersaline environments.