Southern Ocean eddies shape the foraging ecology of marine apex predators such as marine mammals and seabirds. A growing number of animal tracking studies show that predators alter their swimming, diving, and foraging behavior in 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 parts of the world have found that eddies can impact the abundance and community composition of micronekton. Here, we analyze acoustic observations from a 14-day survey of a mesoscale eddy, its surrounding waters, and the Sub-Antarctic frontal waters where the eddy originated. We report and interpret spatial patterns of acoustic backscattering at 18 kHz, a proxy indicating combined changes in species, size, and abundance of micronekton. We find that the vertical distribution of Deep Scattering Layers matched the underwater light conditions characteristic of the eddy core, periphery, and surrounding waters, at scales smaller than 10 km. Furthermore, the average water-column integrated acoustic backscattering values in the eddy core were only half of the values measured in the Sub-Antarctic Zone waters surrounding the eddy. By contrast, the acoustic properties of the eddy core were similar to those measured in the Polar Front Zone, where the eddy originated 27 days before our sampling. These results show that, as for physical and chemical tracers, the eddy maintained its biological characteristics from its source waters creating a unique habitat compared to its surrounding waters.