Inflammatory bowel disease or IBD, affected ۶.۸ million individuals worldwide. Crohn's disease (CD) incidence attempted from ۲۲۰ to ۴۰۰ per ۱۰۰,۰۰۰ individuals, whereas ulcerative colitis (UC) occurrence increased from ۳۹۰ to ۵۷۰ per ۱۰۰,۰۰۰ people. In the current genomics study, we identified the gene expression profile in immune cell populations and the diversity of cells in various tissues by analyzing scRNA-seq data from mucosa and IBD (Crohn's disease) tissues. Method: The ۱۰xGenomice scRNA-seq data (GSE۲۰۲۰۵۲) was analyzed using the Seurat, Celldex and SingleCellExperiment packages in the R programming language. ۲۰,۱۹۱ cells from ۶ samples including: ۳ mucosa and ۳ IBD (Crohn's disease). PCA and UMAP were employed to assess cell categorizing and dimensionality reduction. The singleR package was applied to automatically annotate clusters and identify various cell types. FeaturePlot, VlnPlot, RidgePlot and DimPlot functions were employed for constructing visual illustrations of the different expression and abundance of genes within each cell subtype. Results: Compared to the mucosa tissue, the proportion of NK Cells, Hepatocytes and DC in the IBD tissue (Crohn's disease) was significantly increased and proportion of Tissue Stem Cells, Monocyte, B Cells, Epithelial Cells, Neurons, T Cells and Neutrophils was significantly decreased. (PLCG۲, LRMP = Epithelial Cells), (ADH۱C, MT۱G = Hepatocytes), (GUCA۲B, CA۴ = DC), (DEFA۶, DEFA۵ = Neutrophils), (CXCL۱۴, MMP۱ = Tissue Stem Cells), (S۱۰۰A۸, TIMP۱ = Monocyte), (HIST۱H۴C, STMN۱ = NK Cells), (IGKV۴-۱, IGKC = B Cells), (IFITM۲, PTPRCAP = T Cells) and (CHGA, NTS = Neurons) were highly expressed, respectively, as two biomarkers that are present in IBD tissue (Crohn's disease) and mucosa tissue. Conclusion: According to the critical function these genes in cell division, apoptosis, cell growth and signaling pathways, these genes are utilized in the early detection, target therapy and prevention of crohn's disease (CD) and ulcerative colitis (UC) or Inflammatory Bowel Disease (IBD).