Abstract
The identification of demographically independent populations and the recognition of management units have been greatly facilitated by the continuing advances in genetic tools. Managements units now play a key role in short‐term conservation management programmes of declining species, but their importance in expanding populations receives comparatively little attention. The endangered yellow‐eyed penguin ( Megadyptes antipodes ) expanded its range from the subantarctic to New Zealand's South Island a few hundred years ago and this new population now represents almost half of the species’ total census size. This dramatic expansion attests to M. antipodes’ high dispersal abilities and suggests the species is likely to constitute a single demographic population. Here we test this hypothesis of panmixia by investigating genetic differentiation and levels of gene flow among penguin breeding areas using 12 autosomal microsatellite loci along with mitochondrial control region sequence analyses for 350 individuals. Contrary to our hypothesis, however, the analyses reveal two genetically and geographically distinct assemblages: South Island vs. subantarctic populations. Using assignment tests, we recognize just two first‐generation migrants between these populations (corresponding to a migration rate of