DNA microarry technology provides powerful tools for the genome-wide correlation of gene transcript levels with physiological responses and environmental changes, including global warming and anthropogenic pollution. Gene expression changes are sensitive indicator of such environmental stressors as ecotoxicogenomic view point. However, genome-wide gene expression data are only available in traditional model organisms. To overcome this limit, we introduce the heterologous hybridization to screening the benzo[a]pyrene responsive genes in marine medaka, Oryzias javanicus. As the results, we obtained fifty one differentially expressed gene candidates response to the benzo[a]pyrene (100 ppb) exposure for 24 h. Among these candidate genes, the expression level changes in 26 genes were up-regulated, and 25 genes were down-regulated. These candidate genes have great potential in use as multi-biomarkers for organic pollutants and provide a clue in mechanistic aspects of benzo[a]pyrene toxicity in aquatic animals.