Microsatellites were evaluated as genetic markers for the mitochondrial genome (mtDNA) of Phytophthora cinnamomi for population studies. Two (A)(n) microsatellite loci were cloned from the mtDNA of P. cinnamomi. Amplification products from these loci showed little polymorphism among Phytophthora isolates due to their location in coding regions of mtDNA. A further three (A)(n) microsatellite loci obtained from the complete mtDNA sequence of P. infestans were also not highly polymorphic, although located in non-coding mtDNA. The presence of the (A)(n) microsatellites was not conserved in the genus Phytophthora. Unlike those of the chloroplast genome of plants, (A)(n) microsatellite loci of mtDNA do not have potential as highly polymorphic markers in Phytophthora.