Plant resistance to aphids can be improved by introgressing resistant traits from wild Solanum species into the potato germplasm. Breeding parents are commonly selected from the different accessions of each species. Accessions originate from several seeds collected in a restricted area and are conserved as seeds in genebanks. Genetic heterogeneity may be expected between genotypes from the same accession and could influence resistance level. Working with the potato aphid, Macrosiphum euphorbiae (Thomas), and the accession PI243340 of Solanum chomatophilum (Bitter), which has been previously rated as resistant to M. euphorbiae, we genetically identified and assessed the resistance level of genotypes within the accession. A combination of two multilplex polymerase chain reactions (PCRs) discriminated the 13 plant genotypes assessed. Survival of M. euphorbiae, measured using clip cages, varied significantly between five genotypes, randomly selected among the 13 previously assessed, but did not differ between same-genotype plants. Survival among genotypes ranged from 0 to >60% 12 d after adult molt, and the least resistant genotype exhibited survival close to the susceptible standard, Solanum tuberosum L. Our results support the use of PCR multiplex methods to assess genetic heterogeneity in wild Solanum, and suggest that within accession genetic heterogeneity is sufficient to influence resistance level to aphids. Fine screening at the genotype level is preferable when assessing resistance to aphids.