Objective To explore the dignostic value of the candidate molecular markers in Urothelium carcinoma based on Illumina Transcriptome Sequencing. Methods Candidate genes which were screened with transcriptome sequencing were validated by using real-time fluorescent quantitative PCR in 31 pairs of tumor and normal tissues of Urothelium carcinoma patients from Affliated Hai kou Hospital Xiangya School of Medicine Central South University. Results The four candidate genes (CDH1,VEGFA,PTPRF and CLDN7) in tumor tissues were up-regulated compared with normal groups in samples of sequencing. The relative expression of VEGFA mRNA were higher than that in normal tissues. There were significant difference in two groups (P<0.05). PTPRF and CLDN7 were also up-regulated, but no significant difference was found (P > 0.05). PTPRF was closely related with the recurrence of tumor (P=0.002), and the predict sensitivity and speciality rate were 90.0%and 83.3%respectively. Conclusions CDH1 and VEGFA play important roles in the occurrence and development of bladder urothelial carcinoma, and they may be the possible biomarkers. PTPRF is expected to be a molecular reference recurrent predictor of bladder tumor.