Tephritid fruit flies in the genus Rhagoletis bridge between predictable periods of fruit availability by becoming dormant. To cope with acyclic unpredictable events (e.g., frost, mast seeding, etc), a proportion of the population can undergo prolonged dormancy. In the case of walnut infesting Rhagoletis, host plant-derived cues such as juglone soil concentration vary seasonally in predictable patterns. Here, we examined the effects of host plant parts and derived compounds on emergence rates and dormancy duration of Rhagoletis completa (Cresson), Rhagoletis zoqui (Bush) (Diptera: Tephritidae), and associated parasitoids. Pupae of both species were exposed to walnut leaves, fruit, or fruit and leaves and compared to a control. In a second experiment, R. zoqui were exposed to 10 mg l−1 of juglone applied to pupation medium during four consecutive 4-week time periods under variable combinations of temperature and frequency of exposure. Overall, the presence of fruit resulted in greater overwintering survival of R. completa but had no effect on the duration of dormancy of either fly species. Application of juglone over two consecutive periods produced greater mortality of R. zoqui than the control. Three parasitoid species emerged from R. completa and one from R. zoqui. Duration of dormancy for parasitoids was longer than that of fly hosts. Regardless of treatment, 13.3–18.4% of R. completa pupae and 1.3–2.8% R. zoqui engaged in prolonged (>year) dormancy. Our results indicate that host plant derived cues have little or no effect on survival and duration of dormancy of walnut infesting Rhagoletis, and at the tested concentration juglone is toxic to R. zoqui pupae. Testing the effect of juglone at lower concentrations is necessary to rule out its role as an environmental cue for regulation of dormancy. So far, host plant fruiting phenology appears to play a greater role than host plant derived cues in selecting for fly eclosion times.