Cryptochromes (CRYs) are flavoproteins and play a pivotal role in circadian clocks which mediate behavior of organisms such as feeding, mating and migrating navigation. Herein, we identified novel transcripts in Helicoverpa armigera of six isoforms of cry1 and seven isoforms of cry2 by Sanger sequencing. Phylogenetic analysis showed that the transcripts of cry1 and cry2 align closely with other insect crys, indicating within-species divergence of Hacry. A dn/ds analysis revealed that the encoding sequence of the cry1 was under purifying selection by a strong negative selection pressure whereas the cry2 was less constraint and showed a less strong purification selection than cry1. In general, Hacrys were more abundantly transcribed in wild migrating populations than that in laboratory maintained populations, and expression of the cry2 was lower than cry1 in all samples tested. Moreover, when compared with the migrating parental population, offspring reared in laboratory conditions showed a significant reduction on transcription of the cry1 but not cry2. These results strongly suggest that cry1 was more related to the migration behavior of H. armigera than cry2.