small farmers have played an important role in maintaining genetic resources of traditional varieties. collecting and characterizing germplasm, especially landraces and heirloom varieties, are strategic activities that would create a knowledge base describing the traditional varieties of a given region and reduce the risk of genetic erosion. the objectives of this work were as follows: collect sweet potato roots from rural properties and local markets in rio de janeiro state, brazil; characterize the accessions using rapd and issr molecular markers, comparing the efficiency in discrimination of these two types of molecular markers; and estimate the genetic variability of the population. fifty-nine samples from rural properties and 19 from local markets were studied. a matrix of binary data was developed to analyze the molecular data using the jaccard index to estimate genetic differences among accessions, and clusters were made using the upgma method. the molecular techniques detected genetic variability among the accessions, with cophenetic correlation coefficients (ccc) of 0.80 for rapds and 0.89 for issrs. the rapd and issr marker results corresponded well, with a correlation of 0.55. all of the accessions were considered distinct, which demonstrates that traditional farmers maintain sweet potato genotypes that have good genetic diversity.