Bordetella pertussis is the primary causative agent of whooping cough (pertussis), a respiratory disease most severe in unvaccinated infants. The introduction of vaccines against pertussis dramatically reduced disease incidence worldwide. However, many countries have recently experienced disease resurgence, in part due to genetic divergence of circulating strains. The resulting antigenic mismatch with vaccine references has led many to conclude that B. pertussis is evolving under vaccine-driven selection (1–5). Adaptation of B. pertussis is complicated by the varied administration of whole-cell and acellular vaccines between countries and the diversity of reference strains used for vaccine production (6–8). Here, we report the complete genome sequences of two such strains used in manufacturing pertussis vaccines: B202 (Lederle Laboratories, strain 134) and B203 (Sanofi-Pasteur MSD, strain 10536) (9).