Differential gene expression profiling of the liver tissue of the marine medaka fish, Oryzias javanicus, was performed with a cDNA microarray after exposure to 4-nonylphenol (4-NP, $20{mu}g/L$ for 48 h), which is used in detergents, pesticides, and as an antioxidant in plastics and rubber. We identified 218 differentially expressed genes; the expressions of 117 genes were upregulated and those of 101 genes were downregulated (P<0.05). Among them, the expression levels of two genes, vitellogenin 1 and choriogenin L, were found to be upregulated. Both of which are representative environmental estrogen-responsive gene. The upregulated and downregulated genes were assembled into 21 and 20 functional groups, respectively, based mainly on the eukaryotic orthologous groups (KOG) classification. The same tendencies in gene expression were observed in the results of a real-time quantitative reverse transcription-PCR (qRT-PCR) analysis, which was conducted to examine 32 selected genes. The genes differentially expressed in response to 4-NP were associated with estrogenic signaling, immune responses, nerve cell maturation, cellular stress and detoxification, tumor transformation, glucose metabolism, RNA processing, lipid biosynthesis, and iron metabolism. These differentially expressed genes could be used as molecular biomarkers of biological responses to environmental pollutants, especially endocrine-disrupting chemicals.