The major histocompatibility complex (MHC) class II plays a key role in adaptive immunity by presenting foreign peptides to CD4(+) T cells and by triggering the adaptive immune response. While the structure and function of MHC class II have been well characterized in mammalian, limited research has been done on fishes. In this study, we characterized the gene structure and expression of MHC class II alpha (Lunar-DAA) and II beta (Lunar-DAB) of mangrove red snapper (Lutjanus argentimaculatus). Both genes shared, respectively, a high similarity and typical features with other vertebrate MHC class II alpha and II beta. The phylogenetic analysis of the deduced peptides revealed that both Lunar-DAA and Lunar-DAB were located in the teleost subclass. Western blotting analyses indicated that both MHC class II alpha and II beta were expressed ubiquitously in immune-related cells, tissues and organs, and that MHC class II alpha and II eta chains existed mainly as heterodimers. While it was highly expressed in gills, thymus, head kidney (HK), spleen, head kidney macrophage and spleen leucocytes, MHC class 11 beta chain was expressed with a low abundance in skin, intestine, stomach and heart. The highest expression of MHC class 11 beta in thymus confirmed the conclusion that thymus is one of the primary lymphoid organs in fishes. The detection of MHC class II alpha beta dimers in HK macrophages and spleen leucocytes indicated that HK macrophages and spleen leucocytes play a critical role in the adaptive immunity in fishes. All these results provide valuable information for understanding the structure of MHC class II alpha and II beta and their function in immune responses. (C) 2015 Elsevier Ltd. All rights reserved.