Thermophilic microorganisms are quite attractive for the study of biodiversity and evolutionary process as well as biotechnological applications. These organisms provide significant advantages for industrial and biotechnological processes occurring fast and efficiently at high temperatures. Possible potential also is getting increase thanks to isolation of new strains, determination of new metabolites and their pathway. Within the scope of this study, thermophilic bacterial community was investigated with a combination of classical microbiology and molecular biology approaches including fluorescent in situ hybridization, amplified ribosomal DNA restriction analysis, and polymerase chain reaction of 16S rRNA gene. Archaea and Bacteria domain were screened by Fluorescence in situ Hybridization technique. At the end of culture-dependent methodology, Paenibacillus lactis E3.1 (MK573857), Brevibacillus borstelensis E3.2 (MK573871), Paenibacillus naphthalenovorans E2.2 (MK573627), Paenibacillus sp. E3.5 (MK573870) were obtained. Furthermore, these isolates were screened with regards to protease production capabilities. At the end of screening studies, the highest protease activity (300 U/mg) was observed for Paenibacillus lactis E3.1.