【Objective】MUC13 and FUT1 genes are associated with susceptibility/ resistance to ETEC diarrhea in pre-weaning and weaning piglets, respectively. The goal of this study was to improve breeding of diarrhea resistance in different swine populations through development of MAS technology on the two genes.【Method】In the study, PCR-SNaPshot and PCR-RFLP assay were used for animals genotyping from two swine populations（666 Duroc and 512 Pietrain pigs）for the 2 specialized variants. 【Result and conclusion】The results showed that the favorable allele frequency (FAF) of MUC13 gene was 0.890 and 0.180 in Duroc and Pietrain respectively while the FAF of FUT1 gene was 0.754 and 0.677 respectively. Animals with a favorable allele combination of MUC13 and FUT1 genes were different in Duroc with a frequency of 36.75% and Pietrain with 3.49%. The correlation between genotype and phenotype was analyzed, and the results showed that the gene effect on traits was different in the two populations. For example, there were significantly negative correlations between genotype and somatotype in Pietrain, but no association was found in Duroc. According to the breeding practice, it is recommended to achieve purification of MUC13 gene first, and then follow FUT1 gene in Duroc. It is not suitable for marker-assisted selection of two genes in Pietrain temporarily because the ratio of animals with a favorable allele combination of MUC13 and FUT1 gene is too low.