The Major Histocompatibility Complex (MHC) is a key component of the adaptive immune system of all vertebrates and consists of the most polymorphic genes known to date. However, due to this complexity, MHC has not yet been characterized in many species including any Neotropical cichlid fish. Neotropical crater lake cichlids are ideal models to study evolutionary processes as they display one of the most convincing examples of sympatric and repeated parallel radiation events within and among isolated crater lakes. Here we characterize the genes of MHC class II beta chain of the Midas (Amphilophus) cichlid species complex including Amphilophus citrinellus, A. labiatus, A. xiloaensis and A. amarillo from five lakes in Nicaragua. We designed 19 new specific primers anchored in a stepwise fashion in order to detect all alleles present. We obtained 856 genomic DNA (gDNA) sequences from thirteen individuals and 756 additional sequences from complementary DNA (cDNA) of seven of those individuals. We identified 69 distinct alleles with up to 24 alleles per individual. We also found considerable intron length variation and mismatches of alleles detected in cDNA and gDNA.. Lastly, we created a model of protein structure homology for each allele and identified their key structural components. Overall, Amphilophus cichlids have one of the most diverse repertoires of MHC class II B genes known which could serve as a powerful tool to elucidate the process of divergent radiations, colonization and speciation in sympatry