In temperate regions, the shortening day length informs many insect species to prepare for winter by inducing diapause. The adult diapause of the linden bug, Pyrrhocoris apterus, involves a reproductive arrest accompanied by energy storage, reduction of metabolic needs, and preparation to withstand low temperatures. By contrast, nondiapause animals direct nutrient energy to muscle activity and reproduction. The photoperiod-dependent switch from diapause to reproduction is systemically transmitted throughout the organism by juvenile hormone (JH). Here, we show that, at the organ-autonomous level of the insect gut, the decision between reproduction and diapause relies on an interaction between JH signaling and circadian clock genes acting independently of the daily cycle. The JH receptor Methoprene-tolerant and the circadian proteins Clock and Cycle are all required in the gut to activate the Par domain protein 1 gene during reproduction and to simultaneously suppress a mammalian-type cryptochrome 2 gene that promotes the diapause program. A nonperiodic, organ-autonomous feedback between Par domain protein 1 and Cryptochrome 2 then orchestrates expression of downstream genes that mark the diapause vs. reproductive states of the gut. These results show that hormonal signaling through Methoprene-tolerant and circadian proteins controls gut-specific gene activity that is independent of circadian oscillations but differs between reproductive and diapausing animals.reproductive diapause | photoperiodism | basic helix-loop-helix protein | oogenesis T o cope with adverse winter conditions, animals either migrate or minimize their metabolism and hibernate or diapause (1). Animals including insects anticipate these annual rhythms by measuring the changes in night or day length (i.e., photoperiod) through a seasonal clock whose mechanism has yet to be elucidated (2, 3). The hallmarks of diapause in insects such as the linden bug, Pyrrhocoris apterus, and the bean bug, Riptortus pedestris, include cessation of reproduction (4-6) and changes in the physiology of the digestive system (7) and the fat body (8). The arrest is induced by short days and results in small diapause ovaries. Conversely, long days promote ovarian maturation through the action of juvenile hormone (JH), produced by the corpora allata glands (9-11).JH is an insect sesquiterpenoid that controls reproduction (12) and entry into metamorphosis (13). The connection between JH and reproductive diapause is well documented in various species (14). Application of the JH-mimicking analogue methoprene to diapausing P. apterus or R. pedestris bugs is sufficient to terminate diapause and induce ovarian growth (6, 15). Endogenous JH or added methoprene act through the Methoprene-tolerant (Met) protein to prevent premature metamorphosis in P. apterus juveniles (16). Met is a transcription factor of the basic helix-loophelix Per-ARNT-Sim (bHLH-PAS) family (17), and it has been characterized as a JH receptor (18,19 Whether photoperiodic regulation of seasonal diapause/repr...