Background & objectives: Colon cancer is a common disease in the world that causes high mortality in affected people. The lack of appropriate diagnostic and prognostic markers has led to the failure in early diagnosis of colorectal malignancies. MicroRNAs play an important role in controlling the expression of target genes involved in the development and progression of colon cancer. The aim of the present study was the bioinformatics identification of microRNAs with distinct expression in cancerous and non-cancerous colon samples. Methods: This type of study was theoretical bioinformatics and microarray data of 1513 colon cancer samples with the accession number of GSE115513 were obtained from the GEO site and marker genes were selected by using R program. Target genes of the identified microRNAs were provided by TARGETSCAN software and finally, the graphical network was plotted in Cytoscape software. Results: Analysis of microarray data showed that has-miR-663b, has-miR-650, has-miR-17-5p, has-miR-4539 and has-miR-501-3p have biomarker potential in cancer samples. Statistical analysis and investigation of the target genes indicated that miR-663b (ROCAUC=0. 8965, p=0. 001) and has-miR-650 (ROCAUC=0. 9104, p=0. 001) had significant distinct expression between cancerous and non-tumor margins with biomarker potential. Conclusion: The has-miR-663b and has-miR-650 genes can be used as diagnostic markers to distinguish colon cancer from non-cancerous samples.