Theory predicts that fragmentation will lead to reduced gene flow between populations, with loss of genetic
diversity and increased population differentiation. However, these predictions may not always hold true,
especially for long-lived woody plants and some fig trees (Ficus species) may not be affected by fragmentation
because their fig wasps can transfer pollen for distances of over 100 km. Here we contrast the extent of genetic
isolation caused by fragmentation among three southern African Ficus species with different habitat dependencies
and distributional ranges. Two of the species are restricted to forest environments, which have been
fragmented since at least the Pleistocene, and provide an indication of the long-term genetic effects of forest
fragmentation. The third species is less forest-dependent, with a more general habitat association and more
continuous populations. We found significant population differentiation in all three species. Populations of F.
bizanae, a forest specialist with a highly restricted distribution, displayed the most genetic structure, followed by
the second forest specialist, F. craterostoma. Populations of the habitat-generalist F. sur were the least genetically
structured. Forest specialist Ficus species are clearly not immune to habitat fragmentation, despite extensive
pollen flow, and other southern African forest trees are likely to have experienced similar or greater effects of
habitat fragmentation. The strong genetic structure of F. bizanae suggests a limited seed dispersal range and local
dispersal by the fig wasp pollinator, a possible adaptation to the limited range of its host fig tree.