Pleuragramma antarcticum is the only Antarctic notothenioid characterized by a complete pelagic life cycle and plays a major trophic role in the coastal Antarctic marine ecosystem. A previous genetic study investigated the population structure of this species, but used mitochondrial DNA sequencing and was unable to discriminate between hypotheses of panmixia, with occasional fluctuations of gene pools, and population structure. In the present study, we used 16 EST-linked microsatellites to investigate the population structure of P. antarcticum along the Antarctic Peninsula (AP) shelf, a region of Antarctica highly impacted by regional warming. We found a single gene pool and an absence of inter-annual variability in the southwestern AP, while significant genetic differences were detected on a small geographic scale from samples collected off the tip of the AP, with a signal of increased fragmentation over time. Assignment tests revealed a stronger flow of migrants moving southward along the western AP, following the anti-clockwise Coastal Current, than in the opposite direction. Reduced level of gene flow along the shelf, the increase of population fragmentation with time, and the inability to capture P. antarcticum in the central region of the western AP for two consecutive years, all suggest that this sea-ice dependent species could be highly vulnerable to climate change with possible cascading effects on the Antarctic marine food web.