Large submarine plateaus impede the eastward flow of the deep‐reaching Antarctic Circumpolar Current (ACC), and at the southern Kerguelen Plateau (SKP), the ACC flow is steered north through the Fawn Trough and south through the Princess Elizabeth Trough. During the Kerguelen Axis study, a regional‐scale ecosystem survey, oceanographic sampling showed the ACC water properties west of the SKP to be distinct from those over the SKP. Electrona antarctica, a dominant mesopelagic fish species, is associated with Circumpolar Deep Water transported by the ACC, and modified versions that occur over and downstream from the SKP including along the Antarctic continental slope. Here, otolith chemistry from samples of E. antarctica collected during the survey were used to test a biophysical hypothesis predicting structuring and movement between populations along zonal flow in the ACC. In chemistry deposited during early life in the otolith nuclei, the relationship between MgCa−1 and SrCa−1 showed complete separation between fish collected over the SKP and within the ACC proper, indicating population differentiation. Chemistry from the otolith edges, deposited during the period leading up to capture, showed significantly higher concentrations of MgCa−1 over the SKP, likely related to differences in feeding and reproduction. Fish with nucleus chemistry characteristic of the SKP were also found in samples caught further east, suggesting they were transported along the ACC downstream, and southward toward the Antarctic continent within the Australian–Antarctic Gyre.