Abstract The Penghu Channel (PHC), situated in the southeastern Taiwan Strait (TS), is the major conduit for the South China Sea water (SCSW) and Kuroshio subsurface water flowing into the TS. However, the previous studies in this area were largely focused on the aspects of physical oceanography, with scant attention to the chemical hydrography is poorly studied, and therefore little understood. In order to better understand the seasonal variations of chemical hydrography in the southern PHC, we conducted a systematic survey of chemical hydrography aboard R/V Ocean Research III during cruises in January, March, July and October 2001 as well as March 2002. The water above 200m in the southern PHC is characteristic of salinity and temperature between those of SCSW and Kuroshio water (KW), suggesting it is mixing between these two waters. Nonetheless, the salinity and temperature below 200m are dominated by the SCSW. The relative amount of SCSW and KW flowing into the PHC has varied seasonally and annually. During the transition period of monsoon, KW was more than SCSW, but SCSW had a larger quantity during the northeast and southwest monsoon. The slope of the regression line between the d13CDIC and PO4-3 (0-100m, -0.55; below 100m, -0.30) indicates that the distributions of d13CDIC and PO4-3 in the study area may be controlled by the effect of air-sea exchange or the mixing of different water masses or both. In addition, to evaluate the overall error in d13CDIC analysis, we have checked carefully whether the different storage bottles, the various duration of storage, and different amount of saturated HgCl2 solution added in the water samples would produce uncertainty on the d13CDIC analysis. Our results show no significant discrepancy among these the different treatments, suggesting that the water samples can be stored without measurable d13CDIC change at least for 3 months.