Gene pthA is required for virulence of Xanthomonas citri on citrus plants and has pleiotropic pathogenicity and avirulence functions when transferred to many different xanthomonads. DNA sequencing revealed that pthA belongs to a family of Xanthomonas avirulence/pathogenicity genes characterized by nearly identical 102-bp tandem repeats in the central region. By inserting an nptI-sac cartridge into the tandemly repeated region of pthA as a selective marker, intragenic recombination among homologous repeats was observed in both Xanthomonas spp. and Escherichia coli. Intragenic recombination within pthA created new genes with novel host specificities and altered pathogenicity and/or avirulence phenotypes. Many pthA recombinants gained or lost avirulence function in pathogenicity assays on bean, citrus, and cotton cultivars. Although the ability to induce cell division (hyperplastic cankers) on citrus could be lost, this ability was not acquired on cotton or bean plants. Intragenic recombination therefore provides a genetic mechanism for the generation of multiple, different, and gratuitous avirulence genes from a single, required, host-specific pathogenicity gene.