Stone fruit trees must face a multi-disease and pest challenge context over their entire lifetime, incurring for significant damages and economic losses. To date we actually lack varieties that combine a low level of susceptibility against several of these pests and diseases and more information is still needed to decipher the genetic architecture underlying these resistances for stone fruit trees. Our objective is thus to identify the genetic components of multi-disease resistance of two major stone fruit tree species: apricot and peach. To do so, two core collections composed by 150 apricot and 206 peach replicated accessions are maintained under low phytosanitary conditions respectively in two and three contrasted environments in South-East of France. These accessions have been densely genotyped with the Illumina HiSeq 2000 NGS technique for apricot and the IRSC 16K SNP array for peach. We monitored the multiple symptoms of respectively eight and five pests and diseases over the years since 2020 for apricot and 2021 for peach. Thanks to this integrative phenotyping on several sites and years, we were able to study the interactions between pests and diseases and we successfully identified accessions with lower susceptibilities. After deciphering the effects of genotype, environment and their interactions, we performed genome-wide association studies (GWAS) which allowed us to identify genetic markers linked to resistance to these diverse sources of pathogens. These analyses were conducted jointly on diseases affecting both apricot and peach, such as rust, in order to compare the genetic architecture of disease resistance for these two closely related species. Next steps will include multi-trait GWAS to exploit genetic correlations between traits. This work already paves the way for future marker assisted selection for stone fruit trees in order to make multi-disease resistance a concrete goal for breeders.