The study was carried am in order to determine the phenotypic and genotypic characterization of thermophilic bacteria isolated from Van city Ercis town Hasanabdal hot spring water. Turkey Fatty Acid, rep PCR profiling methods, and 16S rDNA sequence data were used for the molecular characterization of thermophilic bacteria, Totally 9 different bacterial isolates were selected based on morphological, physiological and biochemical tests. These strains were further characterized by molecular tests including fatty acid and rep PCR profiles, and 16S rDNA sequence. Its the Fatty Acid profiles were examined, it was determined that for P13 and P9 isolates, iso-C15:0. anteiso-C15:0. iso-C17:0 and anteiso-C17:0 fatty acids are the major fatty acids. For P22, P86, P56. P60. P59 and P4 isolates, the major fatty acids are C15:0. iso-C16:0, and iso-C17:0 fatty acids, and the major fatty acids for P14, P35 isolates are iso-C15:0 and anteiso-C15:0 fatty acids. These bacterial strains that differ in terms of fatty acid profiles were analyzed by REP and BOX-PCR, which are a genomic fingerprint analysis method. For the strains, which exhibited differences with respect to each other at the end of this analysis, 16S rDNA analyses were performed. As a result of 16S rDNA analyses, it was observed that six of these isolates were identified as Geobacillus pallidus and remaining four strains were Bacillus licheniformis, B. pumilus, Brevibacillus brevis and Br. borstelensis species respectively.