Cytochrome P450 1A (Cyp1a) catabolizes polycyclic organic compounds. In this study, we sequenced the cyp1a gene from two Javanese medaka  Oryzias javanicus  strains and examined gene expression in response to two organic pollutants, phenanthrene and pyrene. Sequence comparisons among the two strains identified several single-nucleotide polymorphisms (SNPs), two of which resulted in amino acid substitutions. Reverse transcription PCR analysis of major organs revealed that the cyp1a mRNA level is highest in the liver. After determining LC 50 s against phenanthrene and pyrene for 96 h (3.9 and 2.5 µM, respectively), cyp1a mRNA expression in the liver against sublethal concentrations of phenanthrene and pyrene was examined. Using quantitative real-time PCR, a positive correlation was discovered between the cyp1a mRNA levels and pyrene concentration, and similar tendency was observed for phenanthrene. cyp1a may serve as a quantitative indicator of a broad range of pollutants.