This study aimed to determine the protein structure and function of FUT1 gene, screen important mutation sites. The physical and chemical properties, and the structure of original and mutant proteins were analyzed to identify important variation loci. A polymorphism analysis of the key variation loci was then conducted among 6 pig breeds. Eight variation loci, including 5 missense mutations and 3 synonymous mutations, were identified in FUT1 CDS. Mutations at M307and M229 were present in most of the potential functional domains and were identified as important variation loci. The polymorphism analysis of M229 detected three genotypes among the 6 pig breeds. Chi-square tests showed that the distribution of M229 genotypes was not significant among the 3 Western commercial breeds, but was highly significant between Chinese native pig breeds and foreign pig breeds. M229 may be an important mutant site of FUT1 and warrants further study as a potentially important genetic marker.