The moose (Alces alces) is the most intensely managed game species in Sweden. Despite the biological and socioeconomical importance of moose, little is known of its population genetic structure. We analyzed 132 individuals from 4 geographically separate regions in Sweden for genetic variability at 6 microsatellite loci. We found evidence of strong substructuring and restricted levels of gene flow in this potentially mobile mammal. F_ST values were around 10%, and assignment tests indicated 3 genetically distinct populations over the study area. Spatial autocorrelation analysis provided a genetic patch size of approximately 420 km, implying that moose less than this distance apart are genetically more similar than 2 random individuals. Allele and genotype frequency distributions suggested a recent bottleneck in southern Sweden. Results indicate that moose may be more genetically divergent than currently anticipated, and therefore, the strong hunting pressure that is maintained over all of Sweden may have considerable local effects on genetic diversity. Sustainable moose hunting requires identification of spatial genetic structure to ensure that separate, genetically distinct subpopulations are not overharvested.