BACKGROUND: Chitinase is responsible for chitin metabolism in a wide range of organisms. However, current knowledge on insect chitinase and their possible functions in relation to low temperature stress is very limited. OBJECTIVE: Six chitinase genes from cold treated desert beetle Microdera punctipennis obtained by RNA-seq technology were characterized, and their expression patterns in different tissues and in response to cold were investigated. METHODS: Multiple sequence alignment was carried out using ClustalW1.81 and Phylogenetic trees were generated by MEGA5. The expression patterns were studied by quantitative real-time PCR. RESULTS: These genes were belong to three different chitinase groups. Almost all of them were highly expressed in midgut, and some are expressed in fat body or hindgut. Subzero-4 degrees C had stronger effect than 4 degrees C in inducing chitinase expression. CONCLUSION: The tissue specific and cold inducible expressions suggest that the chitinases may have diverse functions and play roles in insect cold adaptation.