Most commercial basil cultivars belong to the species Ocimum basilicum L. Moreover, within O. basilicum species, there are five main botanical varieties (var. basilicum L., var. difforme Benth., var. minimum L., var. purpurascens Benth. and var. thyrsiflorum /L./ Benth.) that are mainly found on the market. High levels of both morphological and chemical variability exist within the species due to the intraspecific hybridization and long-term uses throughout the world. The aim of this work was to study the resolving power of morphological traits for reliable identification of basil accessions. Phenotypic dissimilarities between pairs of accessions were calculated, and the unweighted pair-group method dendrogram was constructed. Six clearly defined clusters have been detected, giving a good representation of traditional taxonomic relationships. To compare the efficiency of the morphological traits in accession identification, confusion probability and discriminating power of each trait were calculated. Our results show that with a careful analysis and stringent selection of traits, morphological markers provide an inexpensive and reliable method for routine screening of a large number of accessions, in order to monitor and manage germplasm collections.