Agro-morphologic traits and molecular markers were compared in terms of their discriminating power and informativeness among 17 genotypes assembled in the Cuban avocado germplasm. D parameter adopted for agro-morphological traits was useful for genotype identification. Only four morphological traits were necessary for distinguishing all the individuals analyzed: fruit shape, fruit skin color in mature fruits, harvest season and fruit skin thickness. SSR, AFLP and ISTR markers were powerful techniques for avocado discriminating and varietal identification, but the high level of polymorphic loci detected by dominant markers highlights the discriminating capacity of these genetic markers. With a single AFLP or ISTR primer combination all the individuals were identified. Also, isoenzymes were a low cost technique useful for this purpose in local germplasm. The higher values of expected heterozygosity were detected in codominant markers, but the value for microsatellites doubled or more the ones obtained with isoenzymes and dominant markers. The morphological diversity index was a good estimator of diversity among avocado accessions when variables of high heritability are used and comparable with the expected heterozygosity scored with isoenzymes and DNA markers. The value of this index was very close to those obtained with ISTR and AFLP. The assay efficiency index (Ai) and marker index (MI) had the same pattern of variation than D, I, Iu and P for all molecular markers. Then, both indexes are probably indicators of the discriminating capacity in avocado.