One of the objectives of the ISAFRUIT Project was to perform genetic analyses in four populations of Prunus, two of peach (P. persica) and two of apricot (P. armeniaca), in order to identify major genes and quantitative trait loci (QTLs) for characters related to fruit quality. This required the construction of saturated marker maps in each of these populations. Marker maps were available for an intra-specific peach × peach F2, a BC2 peach × P. davidiana (using peach as the recurrent parent), and an apricot × apricot F1. We have further saturated these maps mainly with SSR (simple sequence repeat) markers. A new map, constructed uniquely from SSRs was prepared for a fourth apricot × apricot F1 population. Using anchor markers, we compared these four maps with the reference Prunus map, constructed using an almond × peach F2 population. As previously observed, conservation of synteny and co-linearity were the general rule, providing additional evidence of the high level of similarity between all Prunus genomes. Comparisons of genetic distances between the maps suggested that those involving similar genomes had higher levels of recombination than those with more distant genomes, particularly the inter-specific crosses. The ISAFRUIT Project is funded by the European Commission under Thematic Priority 5 – Food Quality and Safety of the 6th Framework Programme of RTD (Contract No. FP6-FOOD-CT-2006-016279). Peer reviewed