Objective: Glioblastoma multiform is the most common, aggressive and malignant primary brain tumor with no effective cure so far, and poor prognosis. One of the reasons for this poor prognosis is the extreme sensitivity of tumor cells to hypoxia Materials and Methods: Two glioma cell lines (U87, A172) were cultured in hypoxia condition (1% O2). RNA were extracted and converted into cDNA. Using Klenow DNA Polymerase, cDNA was converted to double stranded DNA. DNA was digested using MspI and MseI restriction enzymes and synthetic linkers were attached to the ends of digestion products. Using linker specific primers, PCR reaction was performed and PCR products were run in polyacrylamide gel. Obtained band patterns were compared with band pattern obtained from cells cultivated in Normoxy condition (20% O2 as a control). Identity of bands which differ, between in the two models, was assessed using sequencing technique. Hereby, genes which have been switched ON or OFF were identified. Results: Based on sequencing results verification with BLAST, we have found a region with high similarity in 6q13-14.3 which may be involved in process of hypoxia in Glioma. Till now no gene has been introduced in this region, Also comparison of sequencing results with miRBase has led us to find 4 miRNAs, Interestingly, at the present no data has been reported about the involvement of these miRNAs in cancer biology. Conclusion: By identification and evaluation of the genes affected by hypoxia and also their related signaling pathways, we can achieve to an infrastructure for designing therapeutic or prophylactic protocol against Glioblastoma.