The wild species associated with the Andean domesticate, the pepino, and closely associated with the wild and cultivated potatoes, are morphologically and ecologically variable. We studied 10 of the 11 known species, represented by 35 accessions, of Solanum section Basarthrum, plus material of two putative new species. Given the morphological variability, and cryptic species, molecular studies were appropriate. Amplified Fragment Length Polymorphisms (AFLP) were utilized because they are highly polymorphic, and cover most of the genome. Some 98% of the 292 fragments recovered proved informative. A neighbour joining cluster analysis and principal coordinates analysis largely supported previous taxonomic distinctions based on decades of morphological and biosystematic study. However, two new distinct molecular elements were identified, one autogamous, the other self incompatible, that will be described as new species, and that mimic a species pair of wild tomatoes native to the same region of Peru. The most diverse taxonomic group, the series Caripensia, also proved to be the most diverse genetically (85% of loci polymorphic), allowing morphologically similar species to be distinguished. The AFLP data and species distributions in this series support an hypothesis of rapid evolution and peripheral isolation as evolutionary mechanisms in the geographically and ecologically diverse series Caripensia.