The guava accessions assembled in the Cuban germplasm collection at Alquízar (Havana Province) were previously characterized by phenotypic descriptors as well as by AFLP DNA markers (Rodríguez et al., 2004; Valdés-Infante et al., 2003). Here, SSR DNA markers were applied in the establishment of phylogenetic relationships. Furthermore, three guava mapping populations were produced by controlled crosses with the dwarf cultivar 'Enana Roja cubana' as the female parent. Based on segregating AFLP markers, an integrated molecular linkage map of guava was constructed for the first mapping population MP1 under investigation. The previously published linkage map (Valdés-Infante et al., 2003) was extended by arranging a total of 220 markers into 11 linkage groups possibly representing the 11 chromosomes (2n = 22) of the guava genome with 11 to 30 markers per linkage group and a total genome length of 1379 cM. QTL analysis for vegetative characters identified a total of fifteen loci contributing to leaf length, leaf width, petiole length, height, and growth rates for diameter and height. The QTL analysis for fruit characters resulted in the identification of loci such as fruit weight, acidity, total soluble solids, vitamin C content, and pulp thickness.