Solanum tuberosum L.belongs to Solanum L. section Petota Dumortier, of which 36% in sect. Petota were polyploid. Many different kind of enzymes or markers were used for the phylogeny of wild diploid and polyploid potatoes, e.g., plastid DNA restriction site, Granule-bound starch synthase (GBSSI), Nitrate Reductase (NIA), Conserved Ortholog setⅡ(COSII). But not so much wild polyploid potatoes were used in these researches. We here conduct a DNA sequencing study, using six nuclear orthologs, of 54 accessions ...