Physalis ixocarpa Brot. ex Hornem. is a native species consumed in many localities of the Cienega-Chapala in the Mexican state of Michoacán. These plants are cultivated into traditional maize crops (Zea mays L.). The fruits are similar to P. philadelphica Lam., but the differences are in the fruit size and organoleptic properties (flavor, sweetness). According to records of domestication that this zone represents in Mexico, it is possible that P. ixocarpa shows incipient differentiation signals in genetic structure and metabolomic fingerprinting. Our objective was to find evidences of genetic and metabolomic differentiation among populations of P. ixocarpa in the Cienega-Chapala. We used the sequencing of the chloroplast intergenic sequences psbJ–petA and trnL–rpL32, and the metabolomic fingerprinting by GC–MS. The results showed that exist genetic differentiation (FST) and signatures of selection (Fu's Fs' neutrality test) among populations. Moreover the metabolomic fingerprinting showed differences among populations and an increase of aldehydes, aromatic aldehydes, ester, and alcohols related with organoleptic properties of P. ixocarpa. We conclude that P. ixocarpa is an important genetic resource with signatures of differentiation in the Cienega-Chapala, Mexico that eventually could be related with domestication signatures.