In contrast to the mammalian major histocompatibility complex (MHC), where the MHC class I and class II loci reside in close vicinity to one another, the bony fishes have unlinked MHC class I and class II. Previous studies in Atlantic salmon have shown specific class I and class II genotypes of MHC that contribute to disease resistance. To learn more about MHC genomics in Atlantic salmon, bacterial artificial chromosome (BAC) clones positive for class I and class II probes were isolated. BAC contig maps of the Atlantic salmon MHC class I and class II regions were constructed and one selected BAC clone from each region was sequenced. BAC clone sequencing reveals an Atlantic salmon classical class Ia genomic region of ~150 kb encompassing the class I UBA locus, the proteosome subunits LMP7, MECL1, LMP2, the transport associated protein TAP2, and the non-immune genes BRD2 (RING3), COLL11A2 and ZNF297. Additionally, the class II like genomic region of ~210 kb encompassed potential class II pseudogenes DAA and DAB, as well as the putative non-immune genes TIP41 and a von Willebrand factor. Unfortunately, the upstream class Ia and the classical class II regions are not represented in the Atlantic salmon BAC library used in this study. The data presented here correlates with the MHC class I arrangements found so far in other bony fish. The described organization may have implications for the underlying genetics governing viral and bacterial disease resistance in Atlantic salmon.