As a first step toward identifying the evolutionary origin of a pathogenic clone of Haemophilus influenzae biogroup aegyptius causing Brazilian purpuric fever, chromosomal variation and genetic relationships were indexed among 17 isolates of biogroup aegyptius and 2209 previously characterized encapsulated H. influenzae strains recovered from 30 countries on six continents. Biogroup aegyptius isolates form three distinct evolutionary lineages of the species H. influenzae and isolates of the case clone are genetically not closely related to other isolates classified as biogroup aegyptius. The Brazilian purpuric fever case clone was found to be genetically allied with H. influenzae isolates producing serotype c polysaccharide capsule. The population genetic evidence suggests that biogroup aegyptius isolates may represent cell lineages occasionally transmitted from nonhuman hosts or spawned from a much larger base population consisting of genetically diverse nonpathogenic precursor clones.