Japanese flounder (Paralichthys olivaceus) is an economic important aquaculture fish that was susceptible to Vibrio anguillarum. To fully deciphered the molecular mechanisms underlying flounder host defense against V. anguillarum infection, we perform the micro-transcriptome analysis of founder spleen with and without V. anguillarum infection at 3 time points. Overall design: The micro-transcriptome was determined for Japanese flounder spleen from V. anguillarum-infected groups (group V) and uninfected groups (group C) at the time points of 6, 12 and 24 h. For each group per time point, three individual fish were used as biological triplicates.