Background: Vascular tumor thrombus is an important pathological feature of malignant tumors, closely related to lymph node metastasis, and considered to be tumor micrometastasis. Two down-regulated genes, Catenin Alpha 3 (CTNNA3) and FERM And PDZ Domain Containing 4 (FRMPD4) were selected via analyzing the differential expression of vascular tumor thrombus in colon adenocarcinoma and paracancerous tissues. Furthermore, we observed the potential role of them in vascular thrombosis of colon adenocarcinoma.Method: Candidate genes for vascular thrombosis of colon adenocarcinoma were screened by GSE127069, and then pan-cancer verification and immune infiltration analysis were performed. The relationship between gene and vascular thrombosis was analyzed from the level of gene mutation by cBioPortal. Finally, the clinical samples collected were used for expression verification.Results: CTNNA3 and FRMPD4 were low-expressed in vascular tumor thrombus of colon adenocarcinoma, which were positively correlated with microsatellite instability (MSI). They were also closely related to immune microenvironment and immune cell subtype infiltration. According to the analysis of gene mutation, their gene deletion was related to the vascular invasion indicator. Finally, the protein and mRNA expression of CTNNA3 and FRMPD4 were down-regulated in the samples of vascular thrombosis of colon adenocarcinoma, compared with the normal glands which from paracancerous tissues.Conclusion: Our study demonstrates that CTNNA3 and FRMPD4 may be potential biomarkers of vascular thrombosis in colon adenocarcinoma. These results may provide a new strategy to identify the micrometastasis in colon adenocarcinoma.