Understanding and harnessing crop genetic diversity is critical for a sustainable use of genetic resources. In peach, the narrow genetic basis in the cultivated pool could threaten future cultivar improvement but extant genetic resources can be mobilized to alleviate this issue. To this aim, populations called core-collections can be created to represent species’ diversity in an optimal way. In this context, we selected a large panel of individuals among elite and exotic peach genetic pools to design a peach core-collection of 206 accessions and aimed at validating its suitability for genetic analyses and resilience breeding. Among them, 192 accessions could be successfully genotyped with the IRSC 16k Illumina SNP-array. Structure analyses via discriminant analysis of principal components and sparse non-negative matrix factorization were congruent and showed the existence of three main genetic groups with moderate admixture, which was coherent with the current knowledge on peach genetic structuration. We also report wide variations in phenology and in leaf spot susceptibility, illustrating the large genetic diversity and breeding potential of this core-collection. Further phenotyping this population in a multisite experimental design under low pesticide cover will allow us to accelerate the discovery of useful variants for resilience breeding.