Insects, like most organisms, have an internal circadian clock that oscillates with a daily rhythmicity, and a timing mechanism (photoperiodic clock) that mediates seasonal events, including diapause. It has been argued that there is a connection between the two clocks. The Mediterranean corn stalk borer moth, Sesamia nonagrioides, undergoes facultative diapause governed by photoperiod. To obtain clues to the link between the molecular mechanism of circadian and photoperiod clocks, we cloned and investigated the expression profiles of the clock genes Snper, Sntim, Sncyc and Sncry1 in the aforementioned moth species. Our previous results suggested that these genes might be implicated in the regulation of the diapause programming in S. nonagrioides. Here we studied the expression patterns of these four clock genes in larvae reared under abnormal non-24 h light-dark cycles (L10:D62 and L10:D14:L10:D62) in order to assess whether disruption of circadian clock would have any effect in the photoperiodic regulation of diapause. In the L10:D14:L10:D62 cycle abnormal expression patterns of the Sntim/Sncry1 and Snper/Sncyc pairs were found, compared to normal 24 h light-dark photoperiods suggesting that individual clock genes are acting independently in the molecular diapause program of S. nonagrioides. Photoperiod therefore appears to be the crucial signal for the regulation of these four genes.