DNAs from 40 strains ofPichia cactophilaandPichia norvegensis, yeasts characteristic of cactus necroses, were compared using randomly amplified polymorphic DNA (RAPD) banding patterns and killer/sensitive phenotypes. Both species belong to the same species complex within the genus. The levels of between-strain RAPD variation were high in both species (higher in the automicticP.cactophilathan in the heterothallicP.norvegensis), although there is little variation in physiological abilities within either species. Although each species was a separate lineage, RAPD analysis confirms that the species are related. Within each species, RAPD variation was related to the geographic origin of the strains.Pichia cactophilastrains from southern Florida were more related to those from Antigua than to those from northern Florida. These results correlated well with the differences among killer/sensitive phenotypes of strains. Principal component analysis indicated that the phenotypes of each species differ. Here too, strains from southern Florida were more similar to those from Antigua than to those from northern Florida. Previous work had identified differences in the cactophilic yeast communities from southern and northern Florida, and these results indicate that the differences are detectable at the population level as well.Key words: RAPD phylogeny,Pichia, killer factor.