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Flatfish is famous for the asymmetric transformation during metamorphosis. The molecular mechanism behind the asymmetric development has been speculated over a century and is still not well understood. To date, none of the metamorphosis‐related genes has been identified in flatfish. As the first step to screen metamorphosis‐related gene, we constructed a whole‐body cDNA library and a whole‐body miRNA library in this study and identified 1051 unique ESTs, 23 unique miRNAs, and 4 snoRNAs in premetamorphosing and prometamorphosing Paralichthys olivaceus. 1005 of the ESTs were novel, suggesting that there was a special gene expression profile at metamorphic stage. Four miRNAs (pol-miR-20c, pol-miR-23c, pol-miR-130d, and pol-miR-181e) were novel to P. olivaceus; they were characterized as highly preserved homologies of published miRNAs but with at least one nucleotide differed …