Electron subantarctic (Electrona carlsbergi) is one of important pelagic myctophidae which circumpolar distributed between the warm waters of the subtropical confluence zone and the Southern Ocean. The distribution, life history and migration pattern of this species were examined using the biological data in 1990s, however, the habitat shift of this species was still unclear. The present study examined Sr:Ca ratio of otolith section for E. carlsbergi from nucleus region to edge and validated the habitat shift of this species using otolith elemental signature analysis. Otolith samples were collected from northern South Shetland Islands during January 2010 (9 individuals), January 2013 (5 individuals) and February 2016 (9 individuals) from krill fishery, respectively. The results demonstrate E. carlsbergi hatched in two different areas, E. carlsbergi with Type I otolith could hatched in the oceanic waters of sub-Antarctic zone and spend the first year of life in this region. Those individuals move across different fronts into the Antarctic waters from the warmer waters after age 1. E. carlsbergi with Type II otolith could hatched in the coastal waters and are transported (or moved positively) across sub-Antarctic Front into the open waters (oceanic regions of APFZ) with the influence of eastward movement of strong ACC system. The present study reveals otolith elemental signature analysis can be used to test habitat shift and life history processes of fish species in the Southern Ocean. Moreover, otolith elemental signature analysis with coupling to water chemistry can be useful to ascertain migration routes of E. carlsbergi.