Air breathing has evolved independently serval times with a variety of air-breathing organs (ABOs) in fish. The Dojo loach (M. anguillicaudatus, Cobitidae) and elongate loach (Leptobotia elongate, Botiidae) are freshwater species in the order Cypriniformes. M. anguillicaudatus has a well vascularized posterior intestine serving as an ABO, while L. elongate can not use posterior intestine to do air breathing. In the present study, we performed a comparative transcriptome analysis of posterior intestine, ABO in M. anguillicaudatus and non-ABO in L. elongate, to understand the gene expression variations in bimodal respiration fish.