Molecular markers have proven to be powerful tools in research related with diversity, variability, and improvement of economically important tropical crops. This study analyzed eight physiological and morphological fruit characters of economic interest in the cultivated Mexican guava (Psidium guajava L.), and assessed the suitability of two sequence specific amplified polymorphism (SSAP) and simple sequence repeat (SSR) markers developed for their use in early selection of individual plants with given fruit characteristics. Principal component analysis (PCA) explained 79% of the morphological variability observed among accessions. S-SAP was more informative than AFLP for studies of variability and diversity in guava, the former marker showing higher percentage of polymorphism (90%) and more intraspecific variability (0.58). It was analyzed by cluster analysis using the unweighted pair group with arithmetic means (UPGMA) method the relationships between accessions from nine guava varieties. S-SAP dendrograms clustered varieties in better agreement with pulp color and fruit shape, suggesting a possible association of the S-SAP marker with quantitative trait loci (QTL) related to fruit physiological and morphological fruit characters. According to results, the microsatellites mPgCIR131, mPgCIR136 and mPgCIR161 might also be linked to QTL related to internal and external pulp thickness, pulp color, and soluble solids, indicating that the SSR markers developed are appropriate for their use in early selection of guava individuals having specific fruit features, therefore being suitable for molecular marker assisted selection (MAS) of the crop. Key words: Microsatellites, quantitative trait loci (QTL), sequence specific amplified polymorphism (SSAP), simple sequence repeat (SSR), Psidium guajava L.