Clock genes are the molecular core of circadian rhythm of vertebrates. In the present study, we investigated the expression of clock genes which contained Arntl1, Clock, Cry1a, Cry3, Cry-dash, Npas2, Npas4, Nr1d1, Nr1d2, Per1, Per3, Rora and Tim in liver and heart of Mandarin fish (Siniperca chuatsi) under the 12h-light and 12h-dark (LD) cycle condition. Melatonin and cortisol levels were also investigated under the same condition. Livers, hearts and plasma of Mandarin fish were collected at ZT0(06:00), ZT3(09:00), ZT6(12:00), ZT9(15:00), ZT12(18:00), ZT15(21:00), ZT18(24:00), ZT21(03:00, 2nd day), ZT24(06:00, 2nd day) (Zone time, ZT) with three fishes at each time point. The total mRNA was extracted from each sample, the semi-quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to determine the temporal changes in mRNA levels. Blood plasma melatonin and cortisol were quantified by competitive ELISA. The data were analyzed both by the One-Way ANOVA (SPSS 17.0) and the cosine function (Matlab 7.0) to investigate the circadian rhythm of these genes. The result indicated that: Cry-dash, Npas4, Nr1d1, Per1 and Tim displayed daily rhythmic expression in the liver. Except for Cry-dash, the expression of the other genes decreased during the light phase and increased in the dark phase. In addition, there were two rhythmic characters of the 9 genes which contained Arntl1, Clock, Cry1a, Npas2, Nr1d1, Nr1d2, Per3, Rora and Tim in the heart of Mandarin fish: 3 genes including Arntl1, Clock and Nr1d2 were reduced at light but increased at dark phase and the mRNA levels of the others sustained low in ZT0 (06:00)-ZT15 (21:00), while increased significantly in ZT15 (21:00)-ZT18 (24:00) and then decreased in ZT18 (24:00)-ZT21 (03:00). Plasma melatonin levels showed a biphasic diurnal pattern, with higher concentrations during the dark phase than the light phase, its lowest level was observed at ZT15 (21:00). Changes in the serum cortisol levels exhibited circadian pattern over a 24h period that the peak detected at ZT18 (24:00) and the trough detected at ZT15 (21:00). In summary, most of the clock genes were expressed in a circadian manner in liver and heart of Mandarin fish (Siniperca chuatsi), with differences in phase and amplitude.