Circadian clocks enable organisms to synchronize their biological processes to environmental daily cycles, thereby increasing species fitness. Components of the molecular clock are conserved across many taxa, though their structure and function can vary. In this study, we aim to investigate the circadian clock of the European flat oyster Ostrea edulis, an endangered species with a pivotal role in biogenic reef ecosystems. Phylogenetic and protein domain analyses were performed to identify orthologues of core clock and clock-associated genes (OeClock, OeBmal1, OePeriod, OeTimeless, OeCryptochrome2, OeRev-erb, OeRor, OeDoubletime, OeClockWorkOrange, OeShaggy), a gene related to melatonin synthesis (OeHiomt) and genes involved in light perception (OeCryptochrome1, OeOpsin4). As a functional output of the clock, we observed daily and circadian rhythms in valve behaviour recorded under light:dark and constant dark conditions. In parallel, gene expression analyses in two tissues under similar light regimes revealed tissue-specific rhythms, suggesting the presence of a functional and plastic endogenous circadian system in O. edulis. These findings offer a first molecular work for deeper exploration of the circadian clock functioning in O. edulis, providing essential resources to investigate its evolutionary adaptation to cyclic environments, and inform restoration and conservation strategies of this threatened species.