13 different MHC class ⅡB alleles which encoded 13 different amino acid seq uences were identified among 411 clones from 42 resistant Japanese flounder individuals and 42 susceptible Japanese flounder individuals using the primer pairs of fmhcN1 and fmhcC1. Among the PCR products of 280 (268) nucleotides, 32 (11.4%) nucleotide positions were variable. Among the putative 61 amino acid sequence, 13 amino acid positions were polymorphic and 6 (46.15%) positions occurred in PBR region. Comparison of the ratio of nonsynonymous substitutions and synonymous substitutions (dN/dS) in the PBR (23.091) and in the NonPBR (0.523) indicated that the selection for amino acid replacement occurred mainly at the PBR region. Phylogenetic analysis using MEGA2.0 software showed that the putative 13 MHC class II B amino acid sequences of Japanese flounder assembled together as a cluster firstly. The phylogenetic relationship with the corresponding sequence of striped sea bass was relatively near, and the phylogenetic relationship with that of mammalian, such as with mouse and human, was relatively distant. With analysis of the occurrence percentages about the 13 different alleles in resistant and sus ceptible stock, most alleles such as Paolallele*aPaolallele*f, Paolallel e*j, Paolallele*k, Paolallele*i, Paolallele*m were commonly found in oth stocks. Using Chisquare Test, Paolallele*d was significantly more prevalent in individuals from susceptible stock than in individuals from resistant stock, and their percentages were 23.80% and 7.14%, respectively. In addition, the Paolallele*g and Paolallele*h only occurred in 13 individuals from 42 resistant individuals, and their percentages were 21.4% and 9.52%, respectively. While Paolallele*l was only found from 42 susceptible individuals, its percentage is 19.05%.