Analysis of meningococcal strains recovered from outbreaks and epidemics in the African meningitis belt, using molecular methods, has demonstrated for nearly 20 years the dominance among serogroup A organisms of a single clone complex, the sequence type 5 (ST-5) complex. However, a shift was observed since the mid-1990s when ST-5 gradually was replaced by ST-7 in all countries of the region. Since 2001, outbreaks caused by serogroup W135 strains belonging to the ST-11 complex became an additional problem. Monitoring of the clones responsible for meningococcal disease provides important insights on the biology and epidemiology of this most serious pathogen.