The population structure of the clouded Apollo butterfly Parnassius mnemosyne was investigated by mark-release-recapture studies and by allozyme polymorphism in north-east Hungary. Large differences were observed in the estimated sizes of different populations. The results of the genetic analysis suggest that even large populations may have small effective population sizes, due to uneven sex ratio, recent bottlenecks and founder effect. The results of both the genetic and MRR studies indicated that the Bukk populations exist as a metapopulation. However, populations from different geographical regions were highly differentiated, indicating restricted gene flow between them. Loss of genetic variability was observed in a small, isolated population. Practical advice is given on how to manage woodland to maintain genetic diversity; it is concluded that many small clearings made close to existing habitat patches is superior to making fewer, larger clearings.