Abstract Objective:Cancer stem cells play an important role in the the drug resistance of malignant tumor and the prognosis, however,the genes that regulate Colon Adenocarcinoma(COAD) stem cells are still unknown. We aim to identify COAD stem cell regulatory genes by co-expression network analysis.  Methods:The mRNA expression-based stemness index(mRNAsi)which derives from TCGA database was analyzed based on R language. The Weighted Gene Co-expression Network Analysis(WGCNA) was used to construct co-expression network, establish the correlation between gene modules and modules trait–mRNAsi , and determine hub genes. We use Enrichment analysis of genes function and Protein Interaction(PPI network)to identifying the hub modules and genes. GEO and OnComine databases were used to validate the hub genes.  Results: MRNAsi was highly expressed in tumor tissues and the result was statistically significant (p = 7.458E-18), and was positively correlated with the survival rate (p =0.016). 6501 genes were screened(FDR<0.05 and|LogFC|≥1)for co-expression analysis and 17 modules were obtained, among which the yellow module had the most significant positive correlation with mRNAsi(p=1e-55,correlation coefficient =0.71).We finally selected 9 genes (BUB1, BUB1B, CHEK1, KIF23, MCM10, NCAPG, NCAPH, PLK4, TTK) from the yellow module as the hub genes. The above genes had a significantly high expression in all 13 tumors in the OnComine database.  Conclusion: The 9 hub genes play a crucial role in the development of COAD and therapeutic resistance.Finding ways to suppress these genes may be a new target for colon cancer therapy by affecting COAD stem cells.