Differential gene expression profiling was carried out using cDNA microarray hybridization on hepatic tissue from marine medaka (Oryzias javanicus) after exposure to benzo[a]pyrene (BaP), a representative polycyclic aromatic hydrocarbon classified as a persistent organic pollutant. Forty-one differentially expressed candidate genes were identified; 18 were induced and 23 were repressed (P/0.05). The genes were assembled into 18 groups based mainly on the Eukaryotic Orthologous Groups classification. These differentially expressed gene candidates could have great potential as molecular biomarkers for identifying environmental stressors and prognosis for the biological effects of BaP. The candidate genes isolated in this study were grouped into endocrine disruption, cardiovascular disease, tumorigenesis, immune response, detoxification, energy production and conversion, and other biological responses. Our results could allow future studies to assess the molecular mechanisms of BaP toxicity and to develop a systems biology approach to environmental stress biology.