Guava (Psidium guajava L.) is one of the economically most important fruit trees of the Myrtaceae. Until nowadays, guava breeding programs in Cuba have been limited to the selection and introduction of genotypes with important agronomic characteristics, but focussed studies on genetic diversity which is very important for the identification of potential parents for breeding programs, had not been undertaken. The utilization of microsatellite (SSR) markers for guava germplasm characterization and gene bank management was the main objective of this work. A total of 34 different SSR alleles ranging from three to seven per locus were detected in the examined genotypes with an average number of putative alleles per locus of 4.57. Out of these, twenty-four alleles were classified as common alleles, out of which 10 were widespread and 14 sporadic. Ten alleles were classified as rare, from which 7 were sporadic and 3 localised. For all SSR loci, a major number of homozygote genotypes were identified, except for the SSR locus mPgCIR09. This result reflected the medium to low levels of heterozygosis detected, which ranged from 0.08 to 0.54 with 0.38 as the total average for this parameter. Genotypes showing cultivar-specific markers were 'Darío 19-2'; 'Belic L-98'; 'BG 76-23'; 'Belic L-205' and 'Microguayaba'. These could be important materials for conservation purposes. The high number of common alleles detected suggested that most of the plant material analyzed shares a common genetic ancestor. The microsatellites evaluated could play an important role in the identification of guava accessions representing an interesting gene pool for ex situ maintenance.