Physalis ixocarpa is an edible species of Solanaceae. This is one of the few cultivated and economically important species of the genus in Mesoamerica. In Mexico, several varieties and landraces have been developed, which have not been molecularly characterized. In the current study, five RAMS primers were used to characterize and assess the genetic variability of two varieties and three landraces of this species. The capacity of these markers to discriminate between them was also evaluated. With comparative aims, Physalis peruviana, the most economically important species of the genus in South America, was analyzed in the same manner. The results revealed that the varieties and landraces of P. ixocarpa conserve important levels of genetic variability (21.75% > Polymorphism < 42.75%), which were higher than that found for P. peruviana (10.75% Polymorphism). RAMS were useful specific markers, as P. peruviana and P. ixocarpa were clearly distinguished one from each other by both cluster analysis and principal components analysis. Close genetic relationships were found between the landraces San Isidro Chihuiro and Verde Puebla, and between the varieties Diamante and Rendidora. In spite of the genetic closeness, the RAMS amplification profiles had a clear varietal-specific tendency, in such a way that they may represent varietal fingerprints, which can be used as authentication tool for varieties and landraces of P. ixocarpa.