Although the leaf-height-seed (LHS) scheme states that plant height and leaf area are closely correlated with seed mass; phylogeny, genome size, growth form, and leaf N may also explain variations in seed mass. Till now, there has been little information on the relative contributions of these factors. We compiled data consisting of 1071 plant species from the literature to quantify the relationships between seed mass, explanatory variables and phylogeny. Strong phylogenetic signals of these explanatory variables reflected inherited ancestral traits of the plant species. Without controlling phylogeny, growth form and leaf N are associated with seed mass. However, this association disappeared when accounting for phylogeny. Plant height, leaf area, and genome size showed consistent positive relationship with seed mass irrespective of phylogeny. Using partial R2s, phylogeny explained 50.89% of the variance in seed mass, much more than plant height, leaf area, genome size, leaf N, and growth form explaining only 7.39%, 0.58%, 1.85%, 0.06% and 0.09%, respectively. Our study is the first to disentangle the contributions of phylogeny and plant attributes to the variance in seed mass, providing a novel avenue for better understanding variation in traits across plant species.