Amphioxus is one of the most ancient species in chordates, and it is believed to associate with the evolutional root of vertebrates. To investigate amphioxus tissues in molecular details would provide insightful information to understand chordates' evolution, the origin and development of vertebrates' organs. We have sequenced transcriptomes of 10 different tissues of Chinese amphioxus (Branchiostoma belcheri), providing a global transcripts expression atlas for further analyses.