The genes of major histocompatibility complex (MHC), the most polymorphic loci known in vertebrates, have become the most studied genes in molecular ecology because they represent one of the best candidates suitable to study natural selection on a molecular level in the wild populations. The extremely high level of MHC allelic diversity is result of many mechanisms, especially the parasite-driven balancing selection, as well as recombination, gene duplication mutation and genetic drift. The main objectives of the present study were: a) to perform a sequence analysis of MHC class IIB alleles in European chub (Leuciscus cephalus), b) to investigate the contribution of evolutionary mechanisms (selection, recombination) to MHC diversity, and c) to analyse the co-evolutionary relationship between metazoan parasite load and MHC class IIB alleles. A total of 311 individuals from 15 populations of chub were collected from European rivers across a wide geographical range. The metazoan parasite load was analyzed at the levels of infracommunity and component community. In order to elucidate the participation of neutral evolutionary mechanisms on maintaining the MHC polymorphism, twelve microsatellite loci and mtDNA (cytochrome b) were analyzed. The associations between metazoan parasites and MHC class IIB alleles were analyzed by using Mantel test and co-inertia analysis (COIA). The results showed an influence of host phylogeny on composition of parasite communities and suggest the relationship between MHC allelic diversity and parasite occurrence. Co-inertia analysis revealed that several MHC alleles are associated to susceptibility to the specific metazoan parasites.