The diversity within 20 rice varieties used as progenitors in Cuban rice breeding programmes was analysed with respect to agro-morphological traits, pedigree and DNA markers. Eleven agro-morphological traits were scored, and phenotypic (Euclidian) distances between the rice varieties were calculated. Sixty random amplified polymorphism DNA (RAPD) and 115 amplified fragment length polymorphism (AFLP) bands served to determine Dice's distance estimates. Cluster analyses were performed based on genetic distance matrices using the unweighted pair-group method of arithmetical means (UPGMA) as the clustering method. This analysis showed five phenotypic, six genealogical, five RAPD and six AFLP diversity groups. Genetic diversity estimates based on RAPD data, but not on AFLP, efficiently represented the genetic parentage and phenotypic diversity between rice varieties. Combined diversity estimates allowed the identification of 11 different genetic pools and permitted a more effective separation of the progenitor set than those obtained solely by phenotypic and genealogical information. The results of this study stress the necessity to diversify rice parental stocks for further breeding purposes.