The largest diphtheria outbreak in the developed world since the 1960s began in the Russian federation in 1990. One hundred fifty-six Corynebacterium diphtheriae strains from throughout Russia, selected for temporal and geographic diversity, were assayed by ribotyping and multilocus enzyme electrophoresis (MEE). These tests showed significant genetic diversity within the C. diphtheriae species, and ribotyping and MEE data generally correlated well with epidemiologic data. A distinct clonal group of C. diphtheriae isolates (ET 8 complex) emerged in Russia in 1990 as the current outbreak began, and as the outbreak has progressed, these organisms have made up increasingly larger proportions of the strains that are isolated. Furthermore, the main characteristic of the epidemic strains is a specific combination of ET 8 and ribotypes G1 and G4. This study confirms the epidemiologic utility of the molecular subtyping methods that detected the epidemic clone and addresses the clone's origin and relation to C. diphtheriae from throughout Russia.