Anthropogenic activities continue to cause massive fragmentation and reduction of forest area worldwide. With fragmentation and reduction of habitat recognized as the greatest threats to biodiversity, the implementation of improved, informed and conservation-based forestry practices is essential, and requires a greater understanding of the responses of different organisms to forest fragmentation. While genetic techniques can add invaluable insights to fragmentation studies they have rarely been employed, particularly for multiple species. In the present study, we combined genetic information, obtained from allozyme loci and anonymous single copy nuclear DNA markers, with ecological data to investigate the impacts of forest fragmentation on two log-dwelling beetles with different life histories, in an ‘islands of bush in a sea of pine’ model, at Tumut in New South Wales, Australia. Both the relatively mobile (i.e. has high dispersal ability and/or broad habitat range) Adelium calosomoides and the less mobile Apasis puncticeps showed reduced mobility and gene flow in fragmented compared to continuous forest: there was significantly greater isolation by distance and stronger local structure revealed by spatial autocorrelation in fragmented forest. Analysis of patch and species characteristics revealed that genetic and demographic structure may be influenced by log degradation class for both species, and number of potential dispersal barriers, distance from continuous forest and desiccation intolerance/moisture preference for Ap. puncticeps. Thus the pine plantation matrix poses a barrier or filter for gene flow and mobility in both beetle species.