Maintaining connectivity in fragmented landscapes is a key principle of biological conservation. Although corridors are a widely accepted approach to connecting populations, their merits are still debated, and they may be impractical in many situations. A focus on management of the vegetation matrix between populations has been advocated as an alternative way to deal with habitat fragmentation and has theoretical support. We combined microsatellite DNA and demographic data to provide an empirical account of how two forms of agricultural land use affect the connectivity of insular populations of an endangered skink in southern New Zealand. The grand skink (Oligosoma grande) lives in small populations (approximately 20 individuals) on rock outcrops separated from one another by 50-150 m of inhospitable matrix vegetation (either native tussock grassland or exotic pasture). Skinks typically dispersed short distances, and the nature of the matrix both quantitatively and qualitatively affected dispersal dynamics. Skink populations in pasture were significantly more genetically structured and had less genetic variation than similar populations in tussock, implying less dispersal between populations in pasture than tussock. Furthermore, although female-biased dispersal was a feature of populations in tussock, no sex bias was evident in pasture. In addition, Bayesian individual-based genetic assignment tests that incorporated prior mark-recapture information revealed that some populations produced many emigrants but received few immigrants, whereas other populations were relatively insular Patterns of dispersal and response to matrix vegetation were complex, and the causes of these patterns deserve attention in future studies of habitat fragmentation. Managing the vegetation matrix may be a practical way to connect animal populations in some situations.