The Itajaí-açu river basin is the most extensive basin in the State of Santa Catarina, covering an area of 15,500 Km2, and it houses an important industrial park of the South of Brazil. The estuarine region receives sediments and pollutants from the entire basin, with an area characterized by high demographic density and intense industrial and fishing activity, making this a critical area for the study of biological indicators. The objective of this study was to present a checklist of the zooplankton species in the estuary of the Itajaí-açu river, identifying the groups of species occurring in the different hydrological domains of the estuary and the morphological description of the dominant species, as the basis for future studies of the group in the region. The zooplankton community was investigated in 131 samples obtained between 2005 and 2007, at 7 collection points in the lower estuary of the Itajaí-açu river. The zooplankton consisted of 13 main taxonomic groups and 132 identified taxa. Three associations of species were identified: (a) the limnic community, dominated by the Cladocerans Bosmina longirostris, Camptocercus dadayi, Ceriodaphnia quadrangula, Ilyocryptus spinifer and Moina minuta and by the Copepods Eucyclops serrulatus, (b) the marine community comprised of the Copepods Acartia lilljeborgi, Centropages velificatus, Oithona ovalis, Oithona plumifera, Paracalanus quasimodo and Temora turbinata, and the Cladocerans Penilia avirostris and Pseudoevadne tergestina, and (c) the mixohaline group, comprised of Copepods, Pseudodiaptomus acutus and Pseudodiaptomus richardi.