The European cultivated potato, Solanum tuberosum subsp. tuberosum, has 6 related cultivated species and more than 200 wild relatives. In Solanum spp., studies of cytoplasmic organelles have been mainly confined to the plastid DNA composition of cultivated and wild species. In this study, 53 genotypes of 30 potato species belonging to the subsections Estoloiifera and Potatoe, 2 tomato species, and a black nightshade genotype were examined using PCR markers to evaluate mitochondrial DNA diversity and assess whether mtDNA variability was correlated with series classification, Geographical origin, ploidy, and endosperm balance number (EBN). The markers used revealed interspecific mtDNA variability in Solanum spp. and identified 13 different haplotypes. Intraspecific variability was also observed in a few species and genomic regions. Cluster analysis allowed arrangement of the 13 haplotypes into 7 subgroups, and statistical association tests showed significant relationships between mitochondrial patterns detected by molecular analysis and ploidy, EBN, and geographical origin. On the whole, the evolutionary patterns for the genomic regions analyzed reflected the species relationships established on the basis of morphological and molecular (nuclear and plastidial DNA) data. The mtDNA variability shown is also important for better characterization of genetic resources for potato breeding.