Phytoplankton respiratory electron transport system (P-ETS) activities were studied in two cruises in Taiwan Strait (Aug. 1997 and Feb. -Mar.1998) and two cruises in Xiamen Harbour (Oct., 1997 and Apr., 1998). Results showed that P-ETS activity in the surface water of southern Taiwan Strait in summer was homogeneous [mean value of 0.106 μlO2/(L⋅h)], inhomogeneous in northern Taiwan Strait in winter. Variation of P-ETS activity in middle part of the Strait was not obvious between summer and winter. Mean P-ETS activity of Xiamen Harbour in autumn was 0.255 μlO2/(L⋅h) with a little higher value in Jiulong River estuary areas. In spring, P-ETS activity was more homogeneously distributed and the mean value was 1.076 μlO2/(L⋅h). P-ETS activity in spring was obviously higher than in autumn in Xiamen Harbour. Vertical distribution of P-ETS in Taiwan Strait was homogeneous at some stations in winter and in summer. An obvious daily variation of P-ETS activity was recorded at Stn 9837, high at midnight and low in the early morning. Significant correlation between P-ETS activity and Chl-a was observed. Results also showed that the ratio of estimated respiratory rate to photosynthetic rate varied seasonally, high in winter (0.41) and low in summer (0.12).