Light and temperature are the major environmental signals for insect circadian rhythms, and it is widely believed that magnetoreceptor (MagR) and cryptochromes (CRYs) participate in orientation behavior of organisms navigating or migrating long distances. Potential mechanisms for the coupling of circadian rhythm and magnetic detection have been discussed but are not known for the serious agricultural pest Agrotis ipsilon (Hufnagel). In this study, one novel MagR gene, designated Ai-MagR, was cloned from A. ipsilon by reverse transcription polymerase chain reaction and RACE-PCR strategies. It encodes a protein that has 131 amino acids and one conserved iron–sulfur cluster-binding domain. In a phylogenetic analysis, Ai-MagR was closely related to its orthologs in the noctuid family. The results of quantitative polymerase chain reaction showed that Ai-crys and Ai-MagR were present in all tested organs and life stages of the moths and that the daily levels of the three genes fluctuated. In 16 h light and 8 h dark, expression of Ai-crys and Ai-MagR followed a circadian rhythm throughout the day, and constant light or dark disturbed this rhythm. At 25 ± 1 ° C, expression of Ai-crys and Ai-MagR also had a circadian rhythm through the day, which was disrupted by cold or high temperature conditions. Based on the results, the two CRYs and MagR may play different roles during the migration of A. ipsilon. Overall, these findings have significant importance for further study of the functions of Ai-crys and Ai-MagR genes and potential control of the black cutworm.