Major histocompatibility complex (MHC) class II genes play important recognition roles in the immune system in vertebrates. We cloned the MHC class II genes A and B in the stone flounder (Kareius bicoloratus). The full-length cDNA and DNA sequences of both genes were obtained, and their characteristic motifs were analyzed. The DNA sequence of stone flounder MHC class II A consists of four exons, while gene B contains six exons. The extra intron in gene B might be a common feature in most of its Acanthopterygii orthologs.