The genome sequencing project revealed presence of two active chalcone synthase (CHS) homologues (At1g02050 and At4g34850) in the model plant Arabidopsis thaliana. We report herein the two genes encode closely related novel plant-specific type III polyketide synthases (PKSs) that produces long-chain alkyl alpha-pyrones. PKS-A (At1g02050) and PKS-B (At4g34850) share significantly low amino acid sequence identity (20-40%) with other type III PKSs, and the phylogenetic tree analysis revealed that they form a separate cluster located closely to those of bacterial type III PKSs. When expressed in Escherichia coli, both PKS-A and PKS-B accepted unusually long (up to the C(20) chain-length) fatty acyl CoAs as a starter substrate, and carried out sequential condensations with malonyl-CoA to produce triketide and tetraketide alpha-pyrones. Interestingly, despite the low sequence identity, homology modeling revealed that the active-site architecture of PKS-A and PKS-B showed similarity to that of a bacterial type III PKS from Mycobacterium tuberculosis.