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To gain a better understanding of the molecular mechanisms regulating pupal diapause of the onion maggot Delia antiqua,PCR-based suppressive subtractive hybridization was performed to identify genes involved in summer and/or winter diapause.A total of 209 unique sequences were obtained including 89 in forward library for winter diapausing pupae and 120 in the reverse library for summer diapausing pupae.76.4% (68/89) and 68.3% (82/120) unique sequences had significant hits to nonredundant proteins database.Gene functional annotation showed these non-redundant sequences are involved in stress response and innate immunity,metabolism and energy,information processing and regulation,binding,food storage,morphogenesis and development,cell skeleton and cycle,protein synthesis and folding.Approximately 28.2% (59/209) transcripts showed no significant similarity to any other sequence in the public databases,probably representing unique genes of the onion maggot.Semi-quantitative RT-PCR revealed that the relative expression levels of 18 genes were comparable between summer and winter diapause.This study elucidates the temperal expression of diapause related genes in onion maggot,also provides new insights into the differences in the physiological changes in summer and winter pupae.Functional characterization of some candidate genes will further enhance the understanding of the generating,maintaining,and breaking mechanism of diapause.