Naranjilla (Solanum quitoense Lam.) is an Andean fruit crop with great economic prospects in global export markets. The conservation and improvement of this crop greatly depend on the quantification of its genetic variability and on finding alternative sources of diversity in the Lasiocarpa section. The main objective of this study was to evaluate the extent to which SSR primer pairs specifically designed for Solanum tuberosum L. could be used in genetic diversity and phenetic studies of S. quitoense and its wild relatives from the Lasiocarpa section. Thirteen nuclear SSR primer pairs, out of 48 tested, were successfully transferred. Seven of these primers produced a total of 25 alleles and an average polymorphic information content (PIC) value of 0.4030. The genetic similarity index (Jaccard) between all accessions analyzed was 0.46 (0.54 dissimilarity), a value expected to increase with a greater sample population and a greater array of SSR primer pairs. Our preliminary UPGMA cluster analysis displayed seven major clusters and reinforces previous claims regarding the phenetic relations of section Lasiocarpa. The most important similarities between our results and the results of previous studies lie in the potential exclusion of S. stagnale from this section and the close genetic relationship that exists between S. candidum and the Asian members of this plant group. Our findings open the possibility for the exploitation of cross-species amplification as a source of SSR markers for this plant group; thus contributing toward current developments aimed at improving and preserving S. quitoense, a crop of great importance to the Andean region.