A genome-wide scan for pig umbilical hernia (UH) was performed in a White Duroc × Erhualian resource population reported by our previously study, which detected two susceptibility microsatellite markers (SWR1928 on SSC7 and SW830 on SSC10) significantly affecting pig UH. Herein, fine mapping studies and identification of susceptibility genes for UH were performed in two different populations. A total of 40 SNPs in 12 positional candidate genes located on the two significant segments were genotyped in the F2/F3 resource population. Quality control of the genotype data and transmission disequilibrium test (TDT) were conducted using Plink v1.07 software. The results showed that g.708G>A in IL16 (interleukin 16) gene and g.10664G>A in CDC73 (cell division cycle 73) gene were significantly associated with pig UH. These two prominent SNPs and another two weakly associated SNPs g.10546A>G and g.10811A>G in CDC73 were also undergone the replication TDT test in the outbred commercial populations. All SNPs in the CDC73 gene were confirmed to be significantly associated with pig UH (P<0.05), including g. 10546A>G and g.10811A>G with extreme significant level (P<0.01). Based on these results, CDC73 should be a susceptibility gene for pig UH according to its biological functions and the molecular pathogenesis of UH.