The invention discloses a MUC4 molecular marker capable of identifying the susceptibility/resistibility to diarrhea of weaned piglet F4 of the western pigs and applicable to the genetic improvement of boars, and the application of the MUC4 molecular marker in breeding anti-diarrhea disease traits of the improved boars. Firstly, an identification of MUC4 polymorphic sites is processed, wherein, g.13383C is greater than T, g.15580A is greater than G, g.21208A is greater than G, and g.26002A is greater than C. Secondly, genotyping determination is applied to each of the polymorphic sites by using the PCR-RELP method. Finally, a haplotype is constructed. The invention detects the four polymorphic sites by the modern molecular biology technique, constructs the haplotype, and selects a favorable haplotype to reserve seeds for individuals by using marker assisted selection (MAS), thus being capable of significantly improving the ability to resist the diarrhea disease of the species weaned piglets and greatly reducing death rate of the weaned piglets.