Summary In contrast to phylogenetic diversity (PD), phytochemical diversity is not often utilised to measure biodiversity, although it forms an important aspect of biotic variation. The aim of this study was to explore phytochemical diversity across the flowering plant order Gentianales and the extent to which PD reliably represents phytochemical diversity. We developed the phytochempy package to facilitate the collection of phytochemical data, including a range of methods for calculating phytochemical diversity. To analyse patterns of phytochemical diversity within the Gentianales, species were grouped based on their native botanical regions. The phytochemical diversity and PD of these groups was then calculated to evaluate the similarities and differences among these measures. Given available presence data on phytochemicals in the Gentianales, we observed strong correlations between PD and the richness and disparity aspects of phytochemical diversity, with weak or no correlations with phytochemical evenness. We also found that, for measures of phytochemical diversity that incorporate evenness, the observed associations are driven by the confounding factor of species richness (SR). PD correlates with phytochemical richness and disparity in the Gentianales, but not with evenness, and SR confounds some of these relationships, showing that PD is not a reliable proxy for phytochemical evenness.