SummaryDocumenting phylogenetic diversity for conservation practice allows elucidation of ecosystem functioning and processes by highlighting the commonality and divergence of species’ functional traits within their evolutionary context. Conserving distinct evolutionary histories has intrinsic value, and the conservation of phylogenetically diverse communities is more likely to preserve distinct or relic evolutionary lineages. We explored the potential for anthropogenic forest fragmentation to act as a selective filter of avian phylogenetic diversity within the community of forest-dependent birds of the critically endangered Indian Ocean Coastal Belt Forest (IOCBF), South Africa. We conducted avian point count surveys during the austral breeding season, and calculated fragmentation metrics of forest structural complexity, patch size and isolation. We constructed a maximum likelihood phylogeny using the combined analysis of two mitochondrial genes and three nuclear markers and measured the influence of the fragmentation metrics on six measures of phylogenetic diversity. Our results indicated that the avian community was variously affected by anthropogenic forest fragmentation, with the different metrics of phylogenetic diversity responding with no definitive overall pattern. However, forest structural complexity emerged as an important metric explaining phylogenetic structuring. While the avian community’s phylogenetic diversity displayed resilience to anthropogenic fragmentation, previous research showed a reduction in functional diversity along the fragmentation gradient. Therefore, we recommend studies that especially aim to guide conservation management, incorporate both phylogenetic and functional diversity measures to sufficiently interrogate communities’ resilience to the threats under investigation.