Ecology Letters (2011) Observational evidence increasingly suggests that the Janzen–Connell effect extends beyond the species boundary. However, this has not been confirmed experimentally. Herein, we present both observational and experimental evidence for a phylogenetic Janzen–Connell effect. In a subtropical forest in Guangdong province, China, we observed that co‐occurring tree species are less phylogenetically related than expected. The inhibition effects of neighbouring trees on seedling survival decreased with increasing phylogenetic distance between them. In a shade‐house experiment, we studied seedling survival of eight species on soil collected close to Castanopsis fissa relative to their survival on soil close to their own adult trees, and found that this relative survival rate increased with phylogenetic distance from C. fissa. This phylogenetic signal disappeared when seedlings were planted in fungicide‐treated soil. Our results clearly support negative effects of phylogenetically similar neighbouring trees on seedling survival and suggest that these effects are caused by associated host‐specific fungal pathogens.