A Peruvian quinoa core collection, containing 103 chosen ecotypes or landraces, was defined on a geographically stratified non-overlapping sampling procedure. The objective was to determine whether this protocol was correct. Hence, a phenotypic distance matrix among 76 accessions from this core collection was created by calculating the difference between each pair of accessions for each characteristic. These 76 accessions were chosen because they had complete data for eight morphological descriptors. The diversity index was calculated by averaging all the differences in the phenotypic value for each quantitative descriptor divided by the respective range, and considering a matching coefficient for the qualitative descriptors, i.e., 0 for characteristics that matched, and 1 if they did not. The total sum of squares from the analyses of variance for the phenotypic diversity index, based on morphological descriptors, was partitioned between and within Peruvian Departments. The between Department cluster variance was smaller (0.0022) than the within Department cluster variance (0.0144), because accessions with the same stem colour or similar inflorescence type and colour were grouped together irrespective of their Department. This was further corroborated by the average linkage cluster analysis, which was performed on the phenotypic diversity matrix to study the pattern of variation and the relationship between the quinoa landraces of this core subset according to their geographical origin. Within each sub-cluster (based on above qualitative descriptors) accessions were ranked by their Department of collection, which indicated that the sampling method was appropriate for choosing accessions for the Peruvian quinoa core collection.