Abstract. The metapopulation framework presumes the habitat of a local population to be continuous and homogenous, and patch area is often used as a proxy for population size. Many populations of pond-breeding amphibians are assumed to follow metapopulation dynamics, and connectivity is mostly measured between breeding ponds. However, the habitat of pond-breeding amphibians is not only defined by the pond but, typically, consists of a breeding pond surrounded by clusters of disjoint summer-habitat patches interspersed with an agricultural/semi-urban matrix. We hypothesise that the internal structure of a habitat patch may change connectivity in two ways: (i) by affecting animal movements and thereby emigration and immigration probabilities; and (ii) by affecting habitat quality and population size. To test our hypotheses, we apply a spatially explicit individual-based model of Moor frog dispersal. We find that the realised connectivity depends on internal structure of both the target and the source patch as well as on how habitat quality is affected by patch structure. Although fragmentation is generally thought to have negative effects on connectivity, our results suggest that, depending on patch structure and habitat quality, positive effects on connectivity may occur.