We performed extensive transcriptome analysis of the tiger pufferfish (Takifugu rubripes) using the next-generation sequencer SOLiD III, and profiled millions of small RNA sequences in somatic tissues and gonads, as well as identifying thousands of miRNAs. The number of miRNAs identified was the highest in fish species reported to date. We also report highly variable isomiR features. Overall design: miRNA expression profiles of 9 tissues (7-somatic tissues and 2-gonads) of torafugu were generated by deep sequencing using SOLiD3.