The present study aims to examine the toxicological effects of phenanthrene in the molecular mechanism in zebrafish. We performed RNA-Seq analysis on zebrafish liver responding to phenanthrene exposure. Genes involved in phenanthrene exposure to zebrafish liver were identified from the transcriptional data. This study provides the completed evaluation of toxic effect of phenanthrene exposure to zebrafish by transcriptional approaches. Our findings could present foundation for further study on molecular mechanism responsible for zebrafish's responses to phenanthrene exposure.