Mesoscale oceanographic features influence the composition of zooplankton. Cyclonic eddies can promote upwelling and production of gelatinous zooplankton, which have critical roles in ocean biogeochemical cycling. We examined variation in assemblages of thaliaceans (salps, doliolids and pyrosomes) among mesoscale oceanographic features at the tropical-temperate boundary of the East Australian Current (EAC) in Spring 2019 and Autumn 2021. The influence of cyclonic eddies was examined in a large offshore cyclonic eddy in 2019 and a newly-formed frontal eddy in 2021. Pyrosomes were most abundant in the offshore EAC jet and salps and doliolids were most abundant in coastal features, including within eddies that were transported offshore. In 2019 Salpa fusiformis increased four-fold over eight days in the large cyclonic eddy and in 2021 doliolids increased >50-fold over two weeks in a chlorophyll-rich coastal eddy while abundances of other thaliaceans remained unchanged or decreased. Correlations between abundances of thaliaceans and chlorophyll-a concentrations across the 102 samples collected during both voyages revealed that doliolids occupy a wider range of chlorophyll-a concentrations than salps. Our observations indicate that doliolids thrive in productive shelf environments, salps occur in less productive shelf waters, and pyrosomes are most abundant in oligotrophic waters of the south Coral Sea.