Integrated parental linkage maps have been constructed in three guava mapping populations ("Enana" × "N", "Enana" × "Suprema Roja" and "Enana" × "Belic L-207") based on AFLP and SSR markers. Between 102 and 119 AFLP primer combinations (PCs) were analysed in each population, generating between 684 and 1163 segregating AFLP fragments. The distribution of parent-specific and common markers indicated that "Enana" is less heterozygous than the other parents and that all parents share a considerable gene pool. In addition, between 28 and 171 SSR PCs were analysed for linkage mapping in these populations. Initially parent specific linked fragments were arranged into linkage groups. In all mapping population, 11 linkage groups (LGs) corresponding to the 11 chromosomes of the haploid guava genome were obtained for each parent. Based on the available SSR markers, combined parental linkage maps of each mapping population were produced using as anchor points allelic SSR fragments and common AFLP fragments. These integrated maps contain between 408 and 850 markers and have lengths of 1885 to 2179 cM, respectively. Average linkage group lengths in these maps vary between 160 and 198 cM and contain on average between 37 and 77 markers. Several identical SSR markers were mapped in various progenies, and potential associations of linkage groups from different populations were detected. In the future, the number of common SSR markers has to be increased in order to achieve full alignment of all individual linkage maps into a high-density reference molecular linkage map of guava.