To investigate unknown molecualr and cellular mechanisms underlying polyphenisms in the migratory locusts, we performed whole transcriptome analysis from 12 different groups. Significantly differentially expressed coding and long non-coding (LNC) RNAs were present according to habitats, phases, and genders. Those differentially expressed coding and LNC RNAs were confirmed by quantitative-realtime-reverse transcriptase PCR. Those identified coding and LNC RNAs could be a target for developing environmental friendly management tools in the near future.