Loche is an ancient landrace of squash from Northern Peru, notable for its vegetative reproduction and lack of seeds in fruits. Studies on this crop have been focused mainly on its nutritional properties and agronomic management. However, very little is known about its genetics. Here, we used 21 simple sequence repeats (SSRs) to assess the genetic diversity and population structure of a collection of 100 samples of loche from three localities in Peru, and 10 samples of related species, C. pepo and C. maxima (110 accessions in total). A total 85 bands were manually scored, obtaining an average of 4.05 alleles per locus. UPGMA clustering method was used to generate a dendrogram, and similar to the principal coordinate analysis (PCoA), it showed a clear identification between the three species of Cucurbita. Discriminant analysis of principal components (DAPC) clustered the 110 accessions into four populations: (i) two of loche, (ii) one of C. pepo, and (iii) one of C. maxima. Genetic diversity (i.e. expected heterozigosity) estimation was conducted considering only the two groups (populations) of loche identified by DAPC algorithm, which was 0.03 as an average. The standardized index of association was greater than zero demonstrating that loche is a clonal population. AMOVA revealed the greatest variation between populations (74.58%) and indicated that variability within populations is 25.42%. Vegetative propagation by means of stem cuttings and cultivation in a very restricted geographical area would explain the rather low diversity of loche. This in turn would suggest that the apparent variation observed in fruit shape may be explained by somatic mutation and/or environmental factors. Our next step is to employ NGS tools on this landrace to develop molecular tools that will promote its modern genetic improvement and sustainable management. However, further studies are needed for a more accurate evaluation of phenotypic traits of this precious crop.