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The population numbers of taiga bean goose (Anser fabalis fabalis) have halved during recent decades. Since this subspecies is hunted throughout most of its range, the decline is of management concern. Knowledge of the genetic population structure and diversity is important for guiding management and conservation efforts. Genetically unique subpopulations might be hunted to extinction if not managed separately, and any inbreeding depression or lack of genetic diversity may affect the ability to adapt to changing environments and increase extinction risk. We used microsatellite and mitochondrial DNA markers to study the genetic population structure and diversity among taiga bean geese breeding within the Central flyway management unit using non-invasively collected feathers. We found some genetic structuring with the maternally inherited mitochondrial DNA between four geographic regions (ɸST = 0.11–0.20) but none with the nuclear microsatellite markers (all pairwise FST-values = 0.002–0.005). These results could be explained by female natal philopatry and male-biased dispersal, which completely homogenizes the nuclear genome. Therefore, the population could be managed as a single unit. Genetic diversity was still at a moderate level (average HE = 0.69) and there were no signs of past population size reductions, although significantly positive inbreeding coefficients in all sampling sites (FIS = 0.05–0.10) and high relatedness values (r = 0.60–0.86) between some individuals could indicate inbreeding. In addition, there was evidence of either incomplete lineage sorting or introgression from the pink-footed goose (Anser brachyrhynchus). The current population is not under threat by genetic impoverishment but monitoring in the future is desirable.

Management of harvested species is of great importance in order to maintain a sustainable population. Genetics is, however, largely neglected in management plans. Here, we analysed the genetics of the bean goose (Anser fabalis) in order to aid conservation actions for the commonly hunted but declining subspecies, the taiga bean goose (A. f. fabalis). We used mitochondrial DNA (mtDNA) and microsatellites to determine the subspecies composition of the Finnish bean goose harvest, as the hunting bag is thought to comprise two subspecies, the taiga bean goose and the tundra bean goose (A. f. rossicus). The latter subspecies has a more stable or even increasing population size. Other eastern subspecies (A. f. serrirostris, A. f. middendorffii) could additionally be part of the Finnish hunting bag. We estimated genetic diversity, genetic structure and sex-biased gene flow of the different subspecies. Most of the harvested bean geese belonged to the taiga bean goose, whereas most of the tundra bean goose harvest was found to be geographically restricted to south-eastern Finland. The mtDNA data supported strong genetic structure, while microsatellites showed much weaker structuring. This is probably due to the extreme female philopatry of the species. The taiga bean goose had lowered genetic diversity compared to other subspecies, warranting management actions. We also detected A. f. serrirostris mtDNA haplotypes and evidence of interspecific hybridization with two other Anser species.