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The emergence of type III polyketide synthases (PKSs) was a prerequisite for the conquest of land by the green lineage.Within the PKS superfamily, chalcone synthases (CHSs) provide the entry point reaction to the flavonoid pathway, while LESS ADHESIVE POLLEN 5 and 6 (LAP5/6) provide constituents of the outer exine pollen wall. To study the deep evolutionary history of this key family, we conducted phylogenomic synteny network and phylogenetic analyses of whole-genome data from 126 species spanning the green lineage including Arabidopsis thaliana, tomato (Solanum lycopersicum),and maize (Zea mays). This study thereby combined study of genomic location and context with changes in gene sequen-ces. We found that the two major clades, CHS and LAP5/6 homologs, evolved early by a segmental duplication event priorto the divergence of Bryophytes and Tracheophytes. We propose that the macroevolution of the type III PKS superfamily isgoverned by whole-genome duplications and triplications. The combined phylogenetic and synteny analyses in this studyprovide insights into changes in the genomic location and context that are retained for a longer time scale with more re-cent functional divergence captured by gene sequence alterations.