Wolbachia is the most frequent gram negative Endosymbiont bacteria belonging to α-proteobacter group which can effect sexual and somatic tissues of arthropods. Due to manipulate the host’s reproductive system can be used as a new method for biological control of insects, bacteria important veterinary disease vectors used. In this study, after collection of scorpion species from field with the help of UV lamp at night, their DNA was isolated and two special primers against 16srDNA and WSP were designed. After setting up PCR conditions with positive control samples, PCR unknown samples were marked. The amplified fragment by agarose gel electrophoresis have shown. Then we have the positive samples sequenced. During our study on 40 Hemiscorpius lepturus scorpions, Twenty-eight of the specimens were positive for Wolbachia bacteria, all of which were positive for both primers WSP and 16srDNA primers. The presence of Wolbachia bacteria in the Hemiscorpius Lepturus scorpion has been proven. This detection was performed by two 16srDNA and WSP genes. The prevalence of the bacterium Wolbachia sp. in Khuzestan province can be due to effects of temperature, which is an inhibitory factor for growth of the bacterium in the arthropods. The presence of Wolbachia in H. lepturus scorpions was approved. The accessions number of 16Sr DNA sequences is KY554756 and wsp gene is KY554757 that deposit in Gen Bank.