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Sinonovacula constricta is an important bivalve with strong photosensitivity and a robust circadian rhythm. To elucidate the light entrainment of the molecular circadian clock in this species, this study identified the clock genes, characterized their tissue distribution, and investigated their transcriptional variations under different light regimes: LD (12 h light/12 h dark cycle), LL (continuous light), and DD (continuous dark). The results showed that the S. constricta clock system consists of seven genes [ Circadian locomotor output cycles kaput (ScClock), Brain and muscle ARNT-like protein (ScBmal), Cryptochrome (ScCry1 and 2), Period (ScPer), and Timeless (ScTimeless1 and 2)] that are closely related to their orthologs in marine mollusks and contained corresponding conserved functional regions, indicating the conserved evolution of the circadian clock among organisms. These genes were expressed in all tissues, with high expression in the labial palps and hepatopancreas, suggesting a complex peripheral biological clock in S. constricta and the critical role of these two tissues in circadian functions. When exposed to different light regimes in labial palps, genes from the positive loop (ScClock and ScBmal) displayed a daily/circadian rhythm under both LD and DD and their acrophases were shifted by 5–7 h, whereas genes from the negative loop displayed daily rhythms (ScCry1 and ScPer) under LD and circadian rhythms (ScCry2 and ScTimeless2) under DD. However, only one gene (ScTimeless2) displayed a circadian rhythm under LL conditions. These results suggest that the S. constricta circadian system may be regulated by different clock genes to adapt to various light environments. Although similar phenomena were observed in the hepatopancreas, markedly different clock gene expression patterns occurred between the two tissues, indicating a tissue-specific regulated circadian system. Collectively, this study reveals how the circadian oscillators of S. constricta respond to light and may promote light environment optimization in the S. constricta farming industry. • The molecular circadian clock was conserved in S. constricta. • A peripheral and tissue-specific clock might exist in S. constricta. • The S. constricta circadian clock was synchronized by photoperiod. • A functional clock exists in S. constricta. [ABSTRACT FROM AUTHOR]