Agro-morphologic traits and molecular markers were compared in terms of their polymorphism level, discriminating power, and informativeness for 23 genotypes assembled in the Cuban guava germplasm collection. AFLP and SSR markers were powerful techniques for guava discrimination and variety identification, but the high level of polymorphic loci detected by the dominant AFLP marker highlights the discriminating capacity of this genetic marker. With a single AFLP primer combination all of the individuals were identified, while only a few genotypes can be differentiated with a single SSR primer combination or by morphological variables. The higher values of expected heterozygosity were detected by SSR. This value doubled the one obtained with AFLP, and reflects the high level of informativeness of this marker, due to the multiallelic and co-dominant nature of SSR; which makes them suitable for diversity studies. The morphologic diversity index provided a good estimate of diversity among guava accessions when phenotypic traits of high heritability were used, and it was comparable with the expected heterozygosity scored with DNA markers. The value of this index was the lowest. The assay efficiency index (Ai) and marker index (MI) had the same pattern of variation than discrimination capacity (D), number of banding pattern (I), number of unique banding pattern (Iu) and number of effective pattern (P) for both molecular markers. Then, these indexes are probably indicators of the discriminating capacity in guava.