Background: The circadian clock for patchoulol synthase (PTS) gene in Pogostemon cablin remains largely unexplored. Objective: The objective of this study is to clone and to investigate the expression of PTS gene from the leaves of P. cablin throughout a day. Materials and Methods: The full-length PTS cDNA was isolated by a combination of reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends in P. cablin. Gene expression profiles across leaves at different time points of P. cablin were evaluated using quantitative RT-PCR. Results: The PTS clone contained a 1659-bp open reading frame coding for 552 amino acids, a 61-bp 5′-untranslated end, and a 219-bp 3′-untranslated sequence. The deduced amino acid sequence was 47%–63% identical with the sequence of other known sesquiterpene cyclases from angiosperms. It was observed that the oscillations of PTS transcript persisted in P. cablin during the daily cycle, with peak expression occurring at 1:00 h, 5:00 h, 7:00 h, 9:00 h, 16:00 h, 19:00 h and 22:00 h. In general, PTS had lower oscillation frequency and transcription abundance at daytime than at night, corresponding with the higher temperature, the lower humidity, and the presence of an ultraviolet index. Conclusion: The PTS gene identified in this study is under clock control, which in turn may provide insight into evolutionary progresses in the green lineage.