Eight Philippine races of Xanthomonas oryzae pv. oryzae have been identified based on virulence phenotypes observed on a set of five differential varieties. One of these, Race 3, was found to consist of two phylogenetically distinct lineages based on DNA fingerprinting analysis. To determine, if the two lineages could be differentiated based on host-specificity, 186 strains of Race 3 were analyzed with additional fingerprints and 76 selected isolates with additional differential rice varieties. The strains were separated into 36 haplotypes clustering in three groups (IS1113-B, -C, and -G) at the 75% similarity level. Isolates varied in their reaction to a rice line carrying the resistance gene Xa7, however, the variability was not consistent within lineage. Aggressiveness of isolates belonging to lineage IS1113-B and -G was significantly greater when tested during the dry season than when tested during the wet season. However, no such differences were evident for isolates from lineage IS1113-C, indicating that environmental effects presumably light and temperature are genotype-specific.