Changes in root morphological traits of seed plants has been typically associated with transitions from the ancestral arbuscular mycorrhizal (AM) to the alternative ectomycorrhizal (ECM) or non-mycorrhizal (NM) associations. However, changes in root morphology also coincide with changes in leaf physiology and growth habit during the diversification of Angiosperms. To explore the evolution of root systems and their role in the diversification in seed plants, we assembled a 600+ species database to reconstruct historical changes in root, leaf and growth form in seed plants. Our findings show important shifts in diameter, specific root length and tissue density as Angiosperms diversified. For most plants, changes in morphology occurred before the acquisition of novel mycorrhizal affiliations, but along with changes in leaf hydraulics and growth form. These findings suggest that adaptation in root systems was crucial during plant diversification and defined important ecological divergences among phylogenetic clades.