Significance Phosphonic acids are organophosphorus molecules containing direct carbon–phosphorus bonds that are often perceived as biological rarities. The data presented here show that the ability to synthesize diverse phosphonates is both widespread and relatively common among microbes. These findings are consistent with recent evidence suggesting that phosphonates are important intermediates in the global phosphorus cycle. Moreover, they support the idea that these molecules play a significant role in the biology of producing organisms, including a mechanism to sequester scarce phosphorus resources and to compete via chemical warfare using toxic phosphonate mimics of common metabolic intermediates.