The main objectives of this study were to test whether there was an association between MHC class IIB (DAB) genes and metazoan parasite infection in European chub populations across its distribution range in Europe. We found significant differences in the metazoan parasite load among the examined European chub populations and also documented a high degree of polymorphism in functional DAB genes. The analysis of twelve microsatellite loci revealed significant phylogeographic population structure. The analyses based on pairwise data revealed that populations with dissimilar MHC allelic profiles were geographically distant populations with significantly different diversity in microsatellites and a dissimilar composition of parasite communities. Further, metazoan parasite load in European chub was influenced by the diversity of DAB alleles as well as by the diversity of neutral genetic markers and host condition and immunocompetence.