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MicroRNAs (miRNAs) are involved in many biological activities including immune defense against pathogens. In this study, we applied high-throughput sequencing technology to examine miRNAs in Japanese flounder (Paralichthys olivaceus) infected with Streptococcus iniae at different times. A total of 1038 miRNAs were identified, of which, 249 were novel miRNAs, and 81 showed differential expression (named DEmiRNAs) after S. iniae infection. Of the 81 DEmiRNAs identified, 34 and 58 occurred at 6 h and 24 h post-infection, respectively; most DEmiRNAs were strongly time-specific, and only 13.6% of the DEmiRNAs were shared between the two time points. A total of 9582 target genes were predicted for the 81 DEmiRNAs. The putative target genes were enriched in various GO and KEGG pathways of biological processes and molecular/cellular functions, in particular endocytosis, regulation of transcription, lysososme, and the signaling pathways of MAPK, ErbB, and AMPK. One of the DEmiRNAs, pol-3p-10740_175, was found to target dual specificity phosphatase 6 (Dusp6) and repress the expression of the latter. Transfection of flounder FG cells with pol-3p-10740_175 caused a significant inhibition on S. iniae invasion. The results of this study provided the first S. iniae -induced miRNA profile in Japanese flounder and indicated that flounder miRNAs play an important role in antibacterial immunity. • Streptococcus iniae infection altered the expression of 81 miRNAs in flounder. • There were 34 and 58 differentially expressed miRNAs at 6 and 24 hpi, respectively. • The putative target genes of the miRNAs were enriched in various GO/KEGG pathways. • One miRNA, pol-3p-10740_175, negatively regulated dual specificity phosphatase 6. • Overexpression of pol-3p-10740_175 significantly inhibited S. iniae invasion. [ABSTRACT FROM AUTHOR]