Ceratocystis manginecans has recently been described from Oman and Pakistan where the fungus causes a serious wilt disease of mango. In both countries, the disease has moved rapidly throughout mango producing areas leading to the mortality of thousands of mango trees. The disease is associated with the infestation of the wood-boring beetle Hypocryphalus mangiferae that consistently carries C. manginecans. The aim of this study was to consider the population structure of C. manginecans isolated from Oman and Pakistan using microsatellite markers and amplified fragment length polymorphisms (AFLPs). Population genetic analysis of C. manginecans isolates from diseased mango tissue and bark beetles associated with the disease in Oman and Pakistan, showed no genetic diversity. The apparently clonal nature of the population suggests strongly that C. manginecans was introduced into these countries as a single event or from another clonal source.