Taiwan waters are oceanographically complex, being characterized by different water masses in the East China Sea, the South China Sea, the Pacific Ocean and the Taiwan Strait, which form contiguous but distinct ecosystems. These ecosystems interact one with another through complex and strong water circulations. The present work investigates the relatively few studied interactions between the local copepod communities and the heterogeneous hydrodynamical regimes. Gathering data from 53 cruises carried out since June 1998 to October 2004 all around Taiwan, this study leads to the mapping of eleven local calanoid assemblages taking into account the physical properties of the environment in which they appeared and the characteristics of their indicator species. Three of these identified assemblages were located in the tropical waters, southwest of Taiwan. First, the assemblage of the 2001 South China Sea sampling cruises revealed a tropical community dominated by Acrocalanus gracilis and Undinula vulgaris . In the other cluster tropical calanoid species such as Labidocera detruncata , Centropages calaninus and Acrocalanus monachus were found. The eight other assemblages were associated with the seasonal dynamics of the water masses north of Taiwan. Although the seasonal characteristics in the north can be subtle, the demarcation between these assemblages was clear. The early spring community is dominated by Calanus sinicus and followed by Temora turbinata since the beginning of summer. September marks a transition period to a new community characterized by the indicator species Acrocalanus gibber . When the north-easterly monsoon prevails in winter it is the turn of the community of northern common species such as Paracalanus parvus and Euchaeta concinna to prevail. In the mean time, Calanus sinicus starts its intrusion from the Yellow Sea and the East China Sea towards the northwest of Taiwan. Thus, according to our results, identified assemblages appear to be good indicators of different, distinctive, water masses.