The potential biomarkers in inflammatory bowel diseases (IBDs) were analyzed from GSE53867 dataset. Differentially expressed microRNAs (DEMs)-genes and protein-protein interaction networks were constructed, and hub genes selected using Cytoscape. Differentially expressed genes were analyzed for GO and Reactome-pathway. Seven DEMs were upregulated in Crohn's disease (CD), 4 downregulated in ulcerative colitis (UC), 8 upregulated and 2 downregulated in IBD. A 620, 2377, and 1821 target-genes were in CD, UC, and IBD, respectively. SOCS3, upregulated by miR-650, was hub gene in CD, induced by cytokines, through NFKB-signalling pathway to mediate ubiquitin-proteasomal degradation. CIRH1A, downregulated by miR-16, was hub gene of UC, acted by impairing ribosome-biogenesis. SKP2 and ASB1, up- and downregulated, by miR-142 and miR-665, respectively, were hub genes of IBD, induced cytokines through activation of TLR- and TNF-signalling pathways to mediate ubiquitin-proteasomal degradation. SOCS3, CIRH1A, SKP2 and ASB1 genes might serve as valuable biomarkers to differentiate CD, UC and IBD.