The Portulacaceae are a monogeneric family with around 100 species distributed around the world. Seed morphology in the group is diverse, but its systematic significance is controversial, and its diversification patterns are unknown. In this study, the seed morphology and size of 63 samples representing 49 species, nine varieties, and two cultivars are evaluated under a phylogenetic framework. Eight seed features (including size) and DNA sequences were analyzed with parsimony and Bayesian methods and seed diversification patterns were estimated using ancestral character reconstruction under a parsimony approach. Analyses of the seed features retrieved an unresolved phylogeny, contrary to the phylogenetic estimate of the DNA data that was consistent with the clades and subclades obtained in previous studies. The analyses of a combined data matrix of seed features and DNA sequence data did not improve nodal support for the relationships within Portulacaceae. Although the hypothesis testing procedures could not reject the monophyly of major clades within Portulacaceae, ancestral character reconstruction analyses showed that the seed features are homoplasious and do not represent synapomorphies for those clades. Some character states were predominantly present in one clade and were rarely found in others. Seed size seemed to be relatively constant throughout the evolutionary history of Portulacaceae (< 0.85 mm long), with multiple independent events of size increase. Although seed features do not reflect the evolutionary history of Portulacaceae, they still have a high taxonomic value, especially when used along with other features.