Circadian clock genes are crucial for generating and sustaining most rhythmic daily functions in the animal kingdom, which entrain the rhythms of biochemical, physiological, and behavioural processes. To better understand the molecular oscillations of the circadian rhythms in darkbarbel catfish ( Pelteobagrus vachellii), we isolated and characterized two circadian clock genes in P. vachellii, period 1 (per1), and period 3 (per3). The circadian clock gene per1 was found to encode a 1 428-amino acid polypeptide, including PER-ARNT-SIM (PAS) dimerisation domains, a PAS-associated C-terminal motif (PAC), a short mutable domain (S/M), and a nuclear export signal (NES). The 4 902-bp per3 cDNA includes an open reading frame encoding a 1 292-amino acid residue polypeptide with a PER-ARNT-SIM (PAS) domain, cytoplasmic localisation domain (CLD), interaction site (TIS), and a nuclear localisation signal (NLS). The per1 and per3 gene was constitutively expressed in all examined tissues. Moreover, per1 expression within a light/dark cycles showed rhythmic expression in the diencephalon, brain, liver and intestine, with the acrophase at 15?15, 12?52, 7?51, and 12?55, respectively. Daily expression of per3 was rhythmic in the diencephalon, brain, liver and intestine, with the acrophase at 8?15, 9?54, 10?39, and 10?25 h, respectively. These findings expand our understanding of circadian mechanism at the molecular level in this species.