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In fragmented landscapes, species persistence within isolated habitat patches is governed by a myriad of species life-history, habitat patch and landscape characteristics. We investigated the inter-specific variation in non-forest gap-crossing abilities of an entire tropical forest-dependent avifauna. We then related this measure of dispersal ability to species life-history characteristics and occupancy data from 31 variable-sized forest patches sampled within the same fragmented forest landscape. A total of 5436 gap-crossing movements of 231 forest-dependent bird species were observed across ten linear forest gaps of varying widths, adjacent to large areas of undisturbed forest. Species persistence in isolated fragments was strongly linked to gap-crossing ability. The most capable gap-crossers were medium to large-bodied species in the large insectivore, frugivore and granivore guilds, matching the most prevalent subset of species in small forest patches. However, some competent gap-crossing species failed to occur in small patches, and minimum forest-patch area requirements were more important in determining patch occupancy for these species. Narrow forest gaps (4–70 m) created by roads and power-lines may become territory boundaries, thereby eliminating home-range gap-crossing movements for many forest species, but permit rarer dispersal events. Wider gaps (>70 m) may inhibit gap-crossing behaviour for all but the most vagile species. Although patch size and quality may be the most important factors in structuring species assemblages in forest fragments, our results show that the degree of patch isolation and permeability of the surrounding matrix also explain which species can persist in forest isolates. Reducing the number and width of forest-dividing gaps; maintaining and/or creating forest corridors and increasing matrix permeability through the creation and maintenance of ‘stepping-stone’ structures will maximise the species retention in fragmented tropical forest landscapes.