The seasonal and spatial changes in species composition and abundance of copepods in relation to environment factors in both Tanshui and Kaoping estuaries were investigated in 2003. In total, 99 copepod species belonging to 8 genera and 3 families and 113 species belonging to 25 genera and 4 families were identified in the Tanshui and Kaoping estuaries, respectively; correspondingly each with the mean abundance of 1680 ¡Ó 403 inds/m3 and 3682 ¡Ó 1274 inds/m3. The species composition of copepods was apparently different between Tanshui and Kaoping estuaries. In the Tanshui estuary, the 6 most dominant copepods, Temora turbinata, Euterpina acutifrons, Canthocalanus pauper, Acrocalanus longicornis, Acrocalanus gibber, and Nannocalanus minor, were all marine species; among them, T. turbinata was the most abundant and contributed 11.9% to the total copepod count. While in the Kaoping estuary, many dominant species were freshwater dwellers, such as Pseudodiaptomus annandalei, Neodiaptomus schmackeri, Microcyclops tricolor, and Paracyclops fimbriatus. P. annandalei was the most abundant species and contributed 8.3% to the total copepods. The dominant marine species in the Kaoping estuary were Pseudodiaptomus marius, T. turbinata, Acartia omorii, Cosmocalanus darwini and Paracalanus parvus. The species composition and abundance of the copepods exhibited noticeable seasonal changes in both estuaries, particularly in the Kaoping estuary, probably related to the intensities of monsoon, rainfull and runoff of freshwater. In the Tanshui estuary, copepod assemblages were short of clear seasonal changes; the dominant species, Temora turbinata, Euterpina Acutifrons, and Canthocalanus pauper were found in all sampling months, with the peak abundance of these species as well as of the total copepods in May and lowest in November. In the Kaoping estuary, the peak abundance was found in February and lowest in August, while P. annandalei and Mongolodiaptomus birula were the most dominant species in these two months, respectively. The copepod (with the exception of Acrocalanus longicornis) abundance in the Tanshui estuary showed insignificant correlation with environmental factors, having significant and negative correlation with temperature. In the Kaoping estuary, on the other hand, most copepods were negatively and significantly correlated with both temperature and salinity.