Purpose: We report the application of NGS for profiling the impacts of PCP exposure on the transcriptome of zebrafish embryos. Methods: mRNA profiles of 10 hpf/24 hpf PCP-treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: At 24 hpf, 6087 transcripts were affected after 200 µg/l exposure, in which 3593 were up-regulated and 2494 were down-regulated, and 1783 transcripts were affected after 5 µg/l exposure, in which 1031 were up-regulated and 752 were down-regulated. At 10 hpf, 2970 transcripts were affected after 200 µg/l exposure, in which 1526 were up-regulated and 1444 were down-regulated, and 1366 transcripts were affected after 5 µg/l exposure, in which 521 were up-regulated and 845 were down-regulated. Conclusions: This study provides a framework for the application of high-throughput RNA sequencing towards characterization of the impacts of PCP on whole zebrafish larval transcriptome. Overall design: Examination of zebrafish embronic transcriptomes with 2 concentrations and 2 durations of PCP treatments.