AbstractQuestionsAlthough the relative importance of climate in abiotic filtering is higher for woody than for herbaceous species assemblages, it is unclear whether this pattern is also reflected between the woody overstorey and herbaceous understorey of forests. The understorey might respond more to small‐scale soil variation, next to experiencing additional abiotic filtering through overstorey effects on light and litter quality. We explored the proportional importance of climate and soil on the species, trait and (functional) diversity patterns of both the forest overstorey and fern and lycophyte understorey.LocationSubtropical forest along an elevational gradient from 850 to 2100 m a.s.l. in northern Taiwan.MethodsWe measured nine functional traits expected to respond to soil nutrient or climatic stress for woody overstorey species and understorey ferns and lycophytes. Next, we performed parallel constrained ordinations on over‐ and understorey species and trait composition, and multiple regression for species and functional diversity, using measured climate proxies and soil variables as predictors.ResultsClimate was more important than soil in predicting the species composition of both vegetation layers and trait composition of the understorey. The stronger than expected effect of climate for the understorey was likely due to fern and lycophytes’ higher vulnerability to drought, while the higher importance of soil for the overstorey trait composition seemed driven by deciduous species. The environmental drivers affected different response traits in both vegetation layers, and the overstorey had additional effects on understorey traits, resuling in a disconnection of community‐level trait values across layers. Interestingly, species and functional diversity patterns could be almost exclusively explained by climate effects for both layers.ConclusionsThis study illustrates that abiotic filtering can differentially affect species, trait and diversity patterns and can be highly divergent for forest overstorey and fern understorey vegetation, and should consequently not be extrapolated across vegetation layers.