During the last years, Fusarium strains have been isolated from shoots and inflorescences of mango trees affected with floral and vegetative malformation in different orchards from the Axarquia region (south of Spain), highlighting the identification of Fusarium mangiferae. With the aim of elucidate epidemiological aspects and design more efficient control strategies, population diversity among the strains of F. mangiferae associated with MMD in Spain was determined by ap-PCR, RAPD-PCR, vegetative compatibility groups (VCGs) and mating type analyses. Three different VCGs were found among the Fusarium mangiferae Spanish isolates, two of them showing similar ap-PCR and RAPD profiles. PCR with primers specific for the mating type (MAT) alleles resulted in amplification of the MAT-2 allele fragment among the majority of the isolates, there being only two isolates MAT-1. This population diversity suggests at least three possible independent introductions of the pathogen into the Axarquia region.