Mating-type genes in the *Citrus*-associated *Phyllosticta* species are highly variable in their sequence content, but the genomic locations and organization of the mating-type loci are conserved. Ancestral state reconstruction suggests that homothallism is the ancestral thallism state in *Phyllosticta*, with a shift to heterothallism in *Phyllosticta* species that are pathogenic to *Citrus*.