Guava (Psidium guajava L.) belongs to the Myrtaceae family and is native to the tropical and subtropical regions of America. It produces a fruit of high nutritional value due to its mineral and vitamin content. During the past 2 decades, classical methods to evaluate genetic variation have been complemented by molecular DNA techniques. There is a great potential for the application of these molecular markers to fruit crops. The objective of this research was to compare results derived from individual versus combined data sets for varietal identification and diversity estimation in guava germplasm by different DNA markers. AFLP data permitted the discrimination of all the accessions evaluated, but diversity groups were not observed. Microsatellite (SSR) markers detected seven diversity groups, although all the accessions could not be differentiated. The combined AFLP and SSR data offered similar results only when AFLP markers were used. Although coincidences were identified in individuals and combined dendrograms, the integration of the information derived by each marker system individually permitted a more accurate estimation of guava germplasm diversity. This corroborates the strengths and constraints of each data set. Thus, the congruence or correspondence among the results derived from individual data sets is the most important point to consider before combining different types of data.