Technical Abstract: While Phytophthora cinnamomi is heterothallic, there are few instances of successful crossing in laboratory experiments and analysis of field populations indicates a clonally reproducing population. In the absence of sexual recombination the ability to monitor mitochondrial haplotypes may provide an additional tool for identification of clonal isolates and analysis of population structure. To determine mitochondrial haplotypes for this species seven mitochondrial loci spanning a total of 6,961 bp were sequenced for 62 isolates representing a geographically diverse collection of isolates with A1 and A2 mating type. Three of the regions were primarily intergenic regions between genes while the remaining loci spanned coding regions. A total of 45 mitochondrial haplotypes were identified with differences due to single nucleotide polymorphisms (SNPs) and length mutations. SNPs were the predominate mutation in the four coding regions and their flanking intergenic regions while SNPs and length mutations were observed in the three primarily intergenic regions. Some of the length mutations in these regions were due to addition/loss of unique sequences while others were due to variable numbers of subrepeats. Network analysis of the haplotypes identified 8 primary clades with the most divergent clade representing primarily A1 isolates collected from Papua New Guinea. With three exceptions isolate grouping in the network corresponded to mating type and previously published isozyme classifications; in network analysis a haplotype representing an A1 mating type (H29) was placed well within the haplotype grouping having A2 mating type, one haplotype (H26) had isolates with two isozyme classifications and one isozyme group was represented on separate network clades, which suggests recombination has occurred in the past. Among the 62 isolates examined several examples were identified of isolates recovered from different geographic regions from the same or similar host having the same mitochondrial haplotype, suggesting movement of isolates via plant material. Analysis of the dataset to confirmed that fewer loci could be sequenced to classify haplotypes.