The major histocompatibility complex (MHC) genes are vital for the adaptive immune response in vertebrates and are widely used in conservation genetics to represent adaptive variation. Accurate genotyping of MHC alleles is essential for effective conservation, particularly for endangered species like the yellow cardinal (Gubernatrix cristata). However, the absence of locus-specific primers and the highly repetitive nature of these genes present a technical limitation when using short-read sequencing technologies. We produced the first high-quality long-read reference genome for the yellow cardinal. This genome reveals sustained high genome-wide heterozygosity despite inbreeding, with homozygosity patterns and effective population size estimates indicating a long-term decline. We identified seven genomic MHC-I loci, while amplicon sequencing with non-locus specific primers had not confirmed more than two MHC-I loci. Our study also revealed mismatches in primer binding sites across multiple loci, emphasizing the need for high-quality, long-read genomic data to understand the genomic architecture of MCH and to accurately assess locus specific MHC variation.