Abstract: Objective : In this study, we adopted the method of DD-PCR and RT-PCR and screen research on didentify molecular mechanism the related genes of chordoma and supplied the tartget genes for the,genetic diagnosis and genes therapy of the chordoma. Methods Methods: The method of mRNA-DD applied to undertake enlargement, purification and sequential analysis for 1 case of straps of differnces in normal paraneoplastic tissues,to identi the related genes of chordoma and chordoma and to screen 18 cases of chordoma by application of RT-PCR. : Results : It was found in results of mRNADD determination that there were 9 fragments of differneces in case of chordoma, and after the sequential analysis for 2 of the 9 fragments, they were found to have the high autoploidy for RNF-11 and CTC-SODMS genes, respectively. The results of screening for total 18 cases of chordoma showed that the expressive differences for RNF-11 and CTCSODMS genes in chordoma and its normal paraneoplastic tissues both had statistical significance (P<0.001), in which the expression of RNF-11 gene increased significantly in the paraneoplastic tissues, while that of CTC-SODMS gene increased apparently in the tissues of chordoma. Conclusions :The RNF-11 gene is possibly the tumor suppresser gene related to chordoma, whereas the CTC-SODM5 gene is possibly the oncogene in relation to chordoma.