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Mesoscale eddies shape the foraging ecology of predators such as marine mammals and seabirds. A growing number of animal tracking studies show that predators alter their swimming, diving, and foraging behavior within mesoscale eddies. However, little is known about how Southern Ocean eddies influence the distribution of mesopelagic micronekton (fish, squid, and crustaceans), which are major prey items of megafauna. Studies in other oceanic regions have found that eddies can influence the abundance and community composition of micronekton. Here, we analyze acoustic observations from a 14-day survey of a cyclonic mesoscale eddy, its surrounding waters, and the Polar Frontal Zone (PFZ) waters where the eddy formed. We report and interpret spatial patterns of acoustic backscatter at 18 and 75 kHz, proxies indicating combined changes in species, size, and abundance of micronekton. We find that the vertical distribution of acoustic backscatter matched the underwater light conditions characteristic of the eddy core, periphery, and surrounding waters, at scales smaller than 10 km. The median water-column integrated acoustic backscatter values in the eddy core were only half of those measured in the Sub-Antarctic Zone waters surrounding the eddy, but similar to those measured in the PFZ, where the eddy originated 27 days prior. These results suggest that, as for physical and chemical tracers, the eddy maintained its biological characteristics from its source waters creating a unique habitat compared to its surroundings.