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Mitochondrial haplotyping has been useful in tracking lineages of <i>P. infestans</i>. Historically, RFLP analysis defined five haplotypes but at a sequence level we observed much greater diversity. Analysis of five mitochondrial loci (3,750 to 5,775 bp) for 101 isolates from geographically diverse areas identified 36 haplotypes. These broadly matched the traditional type I and II haplotypes but exhibited additional subgrouping. Coalescent analysis generated two main clades reflective of haplotype I and II. Within type II, a and b subgroups were distinct but two main groups were resolved for type I; the first had isolates defined as Ia (with RFLPs) and was further divided into two groups broadly corresponding to geographic origin. The second clade had two groups of Ib isolates interspersed by isolates defined by RFLP as Ia. This confirms that restriction analysis is unsuitable for haplotype classification due to convergent evolution at restriction sites not reflecting evolutionary divergence across the mitochondrial genome. Isolates defined as Ic were distinct from the I and II lineages and, along with another novel lineage, formed outgroups. Haplotype evolution within clonal lineages of <i>P. infestans</i> was examined using nuclear SSR loci to define MLGs. PCA revealed groupings of isolates based on geographic origin and haplotype. Examples of conflicts between MLG and mtDNA haplotypes and correlations among haplotype, MLG and geographic distribution will be discussed.<p><p>Keywords: Oomycete, Root-Tuber Crops, Potato