In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl, a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee (FRAC) classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines (OECD test No. 236). At the end of exposure time (96 hours), simultaneous RNA and protein extraction from 10 embryos was performed. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally, potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.