Plant functional traits often vary among species due to multiple factors. Here, using a dataset consisting of 9370 plant species from East Asia, we found that growth form and climate region explained only 1.7% and 0.3%, respectively, of the variance in fruit type, while phylogenetic conservatism explained 79.5%. Furthermore, phylogenetic conservatism was distributed from the base to the tips of the phylogeny, implying that fruit type reflects both ancient and recent phylogenetic relationships. When phylogeny was not considered, growth form and climate region explained 20.6% and 1.5% of the variation, implying that the association between fruit type and growth form is due primarily to phylogenetic conservatism of both traits, as opposed to correlated evolution. Our results highlight the dominant role of phylogenetic conservatism in explaining the pattern of fruit type can be revealed by parsing out the contributions of explanatory variables and phylogeny to the variance in species’ traits.