Studies of microzooplankton dynamics based on the analysis of community taxonomic composition are very time-consuming and manpower demanding. Recent developments in automatic plankton counting technology offer a new way to consider plankton dynamics with straightforward analysis of community size structures. The present study aimed to determine if cell size is a good descriptor of microzooplankton dynamics. The dynamics of the microzooplankton community of the Bay of Biscay (France) at three sites and during four sampling periods was analyzed using three different classification criteria: taxonomy, body size (ng C cell-1) and equivalent spherical diameter (ESD, m). A Mantel test revealed that there was no difference in the characteristics of microzooplankton dynamics when studying either community size structure or taxonomic composition. Moreover, a BIO-ENV analysis confirmed that the biotic and abiotic factors selected for affecting microzooplankton community dynamics were the same among the three classification types. Considering these results, it is argued that microplankton dynamics is well defined by the study of the community size structure. While focusing on microzooplankton size structure seems promising, homogenizing the size descriptor used among studies would be needed in order to make worldwide data comparisons and ESD/biovolume should be favored. © The Author 2011. Published by Oxford University Press. All rights reserved.