Endemic species are broadly defined as organisms that live naturally and exclusively in a specific geographic area. Due to their rarity and adaptation to specific environmental conditions, endemic species have been a focus of biodiversity conservation and ecosystem health assessment. Australian inland waters are inhabited by endemic species of zooplankton including those belonging to rotifers, cladocerans and copepods. Due to their small body size (mostly < 1 mm) and uncertainty in species-level identification, accuracy of population size and geographic distribution of endemic zooplankton species are largely unknown. This leads to a lack of accurate understanding of their ecological significance, even though zooplankton are recognised as a critical food link between primary producers (e.g., algae) and higher consumers (e.g., larval fish). Greater efforts are needed in research and monitoring programs that consider taxonomy, population dynamics and biogeography of endemic zooplankton species. This helps build a robust reference database to fill the knowledge gaps in current biodiversity conservation strategies and ecosystem health assessment in Australian inland waters.