Many species with currently continuously distributed populations have histories of geographic range shifts and successive shifts between decline or fragmentation, growth and spatial expansion. The moose (Alces alces) colonised Scandinavia after the last ice age. Historic records document a high abundance and a wide distribution across Norway in the middle ages, but major decline and fragmentation in the eighteenth and nineteenth centuries. After growth and expansion during the twentieth century, the Norwegian population is currently abundant and continuously distributed. We examined the distribution of genetic variation, differentiation and admixture in Norwegian moose, using 15 microsatellites. We assessed whether admixture has homogenised the population or if there are any genetic structures or discontinuities that can be related to recent or ancient shifts in demography or distribution. The Bayesian clustering algorithm STRUCTURE without any spatial information showed that there is currently a genetic dichotomy dividing the population into one southern and one northern subpopulation. Including spatial information, the Bayesian clustering algorithm TESS, which considers gradients of genetic variation and spatial autocorrelation, suggests that the population is divided into three subpopulations along a latitudinal axis, the southern one identical to the one identified with STRUCTURE. Present convergence zones of high admixture separate the identified subpopulations, which are delimited by genetic discontinuities corresponding to geographic barriers against dispersal, e.g. wide fiords and mountain ranges. The distribution of the subpopulations is supported by spatial autocorrelation analysis. However, some loci are not in Hardy–Weinberg equilibrium and the STRUCTURE analysis suggests that a lower hierarchical structure may exist within the southernmost subpopulation. No bottlenecks or founder events are indicated by the levels of genetic variation, rather a high degree of private alleles in the northern subpopulations indicates introgression. Coalescent-based Approximate Bayesian Computation estimates unambiguously suggest that the genetic structure is a result of an ancient divergence event and a more recent admixture event a few centuries ago. This indicates that the central Scandinavian subpopulation constitutes a relatively recent convergence zone of secondary contact.