Although rarely assessed, the population genetics of hibernating colonies c
an help to understand some aspects of population structure, even when sampl
es from nursery or mating colonies are not available, or in studies of migr
ation when both types of samples are available and can be compared. Here we
illustrate both points in a survey of mitochondrial DNA (mtDNA) control re
gion sequences used to study the population genetics of hibernating colonie
s of a migrating species, the noctule bat (Nyctalus noctula). Lacking sampl
es from Scandinavian nursery colonies, we use a North European hibernacula
to suggest that Scandinavian populations are isolated from Central and East
European colonies. Then, we compare genetic diversities of nursery and hib
ernating colonies. We find a significantly higher haplotype diversity in hi
bernacula, confirming that they consist of individuals from different nurse
ry colonies. Finally, we show that pairwise comparisons of the haplotype fr
equencies of nursery and hibernating colonies contain some information on t
he migration direction of the noctule bat.