Abstract: The HIF (hypoxia-inducible factor) signaling pathway is an oxygen-sensing signaling pathway in animals and plays important roles in metabolism and energy homeostasis under hypoxic conditions. In this study, four key genes of HIF signaling pathway—HIF-1α, HIF-1β, PHD2A and PHD2B were cloned from Sinonovacula constricta using PCR. The physicochemical properties and domains of their encoded proteins were predicted, and their phylogenetic relationships were analyzed. The results showed that HIF-1 contained typical HLH, PAS, PAC, and C-TAD domains, HIF-1α specific ODDD and N-TAD domains, and ScPHD2 contained zf-MYND and P4Hc domains; unlike other invertebrates, shellfish including S. constricta PHD2 had two copies. Using real-time quantitative PCR (RT-qPCR), the expression levels of HIF-1 and PHD2 were further analyzed at different developmental stages, in different tissues of adults and under hypoxia stress (0.5 mg/L and 2.0 mg/L) as well as air exposure stress (21 ℃ and 4 ℃) stresses. The results indicated that S. constricta HIF-1 and PHD2 were expressed from the egg stage, ScHIF-1α was expressed at higher levels than the other genes in the six tissues examined, with the highest expression in gill, followed by hepatopancreas, whereas ScPHD2A and ScPHD2B were expressed at very low levels in all six tissues. Under hypoxia stress, the expressions of ScHIF-1α and ScPHD2 were significantly up-regulated, with a greater up-regulation in the 0.5 mg/L group than in the 2 mg/L group, while ScHIF-1β expressions did not significantly changed. Under air exposure stress, ScHIF-1β expression remained unchanged, whereas ScHIF-1α and ScPHD2 expression were significantly up-regulated, with a stronger up-regulation in the 4 ℃ air exposure group than in the 21 ℃ group. These findings demonstrate that ScHIF-1 and ScPHD2 possessed typical characteristics of the HIF and PHD family, respectively, and their expression is induced to be up-regulated under hypoxia, suggesting that they may be involved in the response process of S. constricta after low oxygen stress. This study provide a reference for further research on the hypoxia signaling pathway and the adaptation mechanisms of S. constricta to hypoxic conditions.