RNA-seq or whole-transcriptome profiling is emerging as a preferred strategy for non-model organisms and this approach gives a detailed information on protein-coding transcripts and expression. Here, we present a large scale and multi-tissue (ovary, testis, kidney, liver and juvenil) transcriptome for E. encrasicolus using RNA-Seq. In addition to providing comprehensive transcriptomic data set, identifying positively selected sites in protein coding regions by comparative evolutionary analysis with other fish species provides a good starting point for understanding egg production in highly fecundate fishes.