To obtain the whole transcriptome of miRNAs in Nile tilapia, the total RNAs were extracted from the fertilized oocytes, 2 post-fertilization (hpf), 4 hpf, 24 hpf, 48 hpf, 72 hpf, 1 day post-hatching (dph), 7 dph , the tissues and organs (skeletal muscle, skin, heart, liver, kidney, gill, gut, stomach, intestines, and eye) of 1 or 2-year-old adult fish, respectively. The equal concentrations of RNAs from different samples were pooled together to construct the small RNA library. Deep sequcing technology and in-depth bioinformatics analysis was used for the systematic discovery of Nile tilapia miRNAs.