Assessing diversity across and within crop varieties is relevant to improve the description of collections in genebanks and in on-farm conservation. The differences among and within several common bean (Phaseolus vulgaris L.) landraces, collected from and maintained ex situ in NE Italy, were initially studied using a set of 15 phenotypic descriptors. From a subgroup of five bean accessions, microsatellite genotyping was performed after the extraction of DNA from each of 38–40 individuals. One of the 15 phenotypical descriptors (plant architecture) was of no use. Only ten out of the 23 molecular markers did work, however sufficient to discriminate the accessions. The phenotypic descriptors identified a portion of the within-population variability. A few discrepancies were obtained when observations of phenotype descriptors were run independently in two alpine locations in NE Italy. The genetic approach carried out separately on DNA of about 40 individuals clarified the structure of the five accessions.