Solanum section Petota, the potato and its wild relatives, includes about 200 wild species distributed from the southwestern United States to central Argentina and adjacent Chile, with about 30 species in North and Central America. The North/Central American region and the South American region all include diploids, tetraploids, and hexaploids. Chloroplast DNA restriction enzyme data from a prior study showed that 13 of the North/Central American species formed a clade containing only diploids, but there was low resolution within the clade. This Amplified Fragment Length Polymorphism (AFLP) study is conducted to provide additional resolution within the North/Central American diploids and complements the chloroplast results, and prior morphological results. Wagner parsimony and phenetic analyses mostly agreed with the morphological data in supporting currently recognized species except that they suggest that S. brachistotrichium and S. stenophyllidium are conspecific. Our new AFLP data, in combination with the cpDNA and morphological data, also support sister taxon relationships for the following diploid species from North and Central America: 1) S. cardiophyllum subsp. ehrenbergii and S. stenophyllidium, 2) S. tarnii and S. trifidum, 3) S. jamesii and S. pinnatisectum, 4) S. lesteri and S. polyadenium, and 5) S. clarum and S. morelliforme.