We compared seedlings of sandy-soil specialist species (Dryobalanops aromatica and Scaphium borneense) and clay-rich-soil specialist congeners (D. lanceolata and S. longipetiolatum) in a tropical rain forest in Lambir Hills National Park, Malaysia, to determine whether variations in belowground seedling architecture and allometry were related to edaphic specialization. A convergent trait that was phylogenetically independent across the two genera was the presence of a deeper tap-root at any height and any root biomass in sandy-soil specialists than in clay-rich-soil specialists. This trait was fixed independently of the edaphic conditions in which the trees actually grew. Finer-textured soils generally have better water-holding capacity; we concluded that seasonal water limitation would be more severe in sandy soils than in clay-rich soils, and that water limitation would provoke convergence in seedling root depth among species with the same edaphic preferences. All significant differences found in interspecific comparison within Dryobalanops were consistent with the water-availability hypothesis; the sandy-soil specialist had larger root biomass at any total biomass and had smaller leaf biomass at any root biomass than the clay-rich-soil specialist. However, for Scaphium this was not the case, suggesting that factors other than water-limitation may also underlie seedling allometric relationships.