Cercospora leaf spot of olives is a serious defoliating disease attributed to Pseudocercospora cladosporioides. Although the disease is well distributed throughout olive growing regions of the world, its epidemiology and population structure remains unknown. The aim of this study was to establish the genetic variability of Spanish isolates of P. cladosporioides using DNA sequence data from the ITS region, as well as two protein-coding genes, actin and calmodulin. Phylogenetic data obtained here support P. cladosporioides as closely related to other Pseudocercospora species that cluster within Mycosphaerella. Spanish isolates clustered in two clades: isolates from Catalonia were different from those collected in Andalusia. However, isolates appeared to be genetically relatively homogeneous, suggesting that chemical control of this disease via a managed spraying programme may prove a viable option for controlling the disease in Spain.