Differential gene expression profiling was performed using cDNA microarray hybridization on the hepatic tissue of the marine medaka (Oryzias javanicus) after exposure to toxaphene, which is classified as a persistent organic pollutant. Ninety-seven differentially expressed candidate genes were identified; 40 were induced and 57 were repressed (P<0.05). The genes were assembled into 18 groups based mainly on the Eukaryotic Orthologous Groups classification. These isolated gene candidates were differentially expressed and therefore have great potential as molecular biomarkers for identifying environmental stressors and prognosis for the biological effects of the toxicant. Some of the genes were closely related to endocrine disruption, renal and cardiovascular disease, tumorigenesis, immune responses, and detoxification. Our results will allow future studies to assess the molecular mechanisms of toxaphene toxicity and to develop a systems biology approach to environmental stress biology.