Diapause is a period of suspended development at a specific period of the life cycle, in order to avoid times that are unfavourable for activity. In the codling moth (CM) Cydia pomonella, an overwintering diapause occurs in the fifth larval instar, and termination of diapause in the spring is indicated by ecdysis and pupation. There is geographic variation as well as large within-population variation (up to 90 days) in the timing of diapause termination in this species. Accompanied by 15 years of observing diapause termination of a CM field population, an artificial selection for early and late diapause termination resulted in two inbred strains, ES (Early strain) and LS (Late strain) which differ in pupation timing after diapause by nearly 90 days. We have initiated a genetic study utilizing most of the possible intercrosses and backcrosses of these two strains and analysed the possible contributions of the autosomes (A) and the sex chromosomes (Z, W) by considering their relative effects on diapause termination time. A large effect of the Z chromosome can be detected because of its unique sex-associated inheritance pattern. Deviations from Z-based predictions can be detected in crosses where ES- and LS-derived autosomes segregate independently from the Z chromosomes. However, not all predictions based on chromosomal inheritance alone are borne out by the data, suggesting involvement of maternal effects, epigenetics, epistasis, or genetic heterogeneity in one or both of the parent strains. These predictions are the basis of further studies to design a cost-effective approach to linkage mapping, to eventually identify the underlying genetic variation causing differences in diapause termination time.