Solanum demissum is a homozygous, hexaploid wild species (2n = 6x = 72, AADDD(d)D(d)) that has long been used as a source of late blight resistance by repeated backcrossing with S. tuberosum (2n = 4x = 48, AAA(t)A(t)). To understand how S. demissum germplasm is incorporated to S. tuberosum through backcrosses, a linkage analysis of 590 DNA markers from S. demissum-specific simplex alleles was performed in an aneuploid population of 87 BC1 plants. Five hundred eighty-one markers were mapped to 38 linkage groups, of which 37 were assigned to potato chromosomes using markers of known location. Three homoeologous chromosomes were distinguished for each of the 12 potato chromosomes. Approximately 50 % of the markers were transmitted to the BC1 progeny except for chromosomes 2c, 3b and 6c, which were significantly under-represented. Two of the three homeologous chromosomes in at least nine of the chromosomes were transmitted to the BC1 progeny with negative correlations, which demonstrated that the two homeologous chromosomes paired at meiosis in the F-1 parent then separated into different gametes. Therefore, we suggest that the two negatively correlated chromosomes were the slightly differentiated genomes cytologically designated D and D-d genomes, while the remaining one was the one cytologically designated A genome of S. demissum. The S. demissum genome map will be useful in analyzing intra-locus interaction of qualitative and quantitative traits among homoeologous chromosomes and analyzing allelic variation of homeolog expression.