Rice produces many diterpenoid phytoalexins and, reflecting the importance of these natural products in this important cereal crop plant, its genome contains three biosynthetic gene clusters (BGCs) for such metabolism. The chromosome 4BGC(c4BGC) is largely associated with momilactone production, in part due to the presence of the initiatingsyn-copalyl diphosphate (CPP) synthase gene (OsCPS4). Oryzalexin S is also derived fromsyn-CPP. However, the relevant subsequently actingsyn-stemarene synthase gene (OsKSL8) is not located in thec4BGC. Production of oryzalexin S further requires hydroxylation at carbons 2 and 19 (C2 and C19), presumably catalyzed by cytochrome P450 (CYP) monooxygenases. Here it is reported the closely related CYP99A2 and CYP99A3, whose genes are also found in thec4BGCcatalyze the necessary C19-hydroxylation, while the closely related CYP71Z21 and CYP71Z22, whose genes are found in the recently reported chromosome 7BGC(c7BGC), catalyze subsequent hydroxylation at C2α. Thus, oryzalexin S biosynthesis utilizes two distinctBGCs, in a pathway cross-stitched together byOsKSL8. Notably, in contrast to the widely conservedc4BGC, thec7BGCis subspecies (ssp.) specific, being prevalent in ssp. japonica and only rarely found in the other major ssp. indica. Moreover, while the closely relatedsyn-stemodene synthaseOsKSL11was originally considered to be distinct fromOsKSL8, it has now been reported to be a ssp. indica derived allele at the same genetic loci. Intriguingly, more detailed analysis indicates thatOsKSL8(j)is being replaced byOsKSL11(OsKSL8i), suggesting introgression from ssp. indica to (sub)tropical japonica, with concurrent disappearance of oryzalexin S production.Supplementary InformationThe online version contains supplementary material available at 10.1007/s42994-022-00092-3.