This dataset corresponds to the SSR (microsatellite) genotypes of a large set of Prunus brigantina and Prunus cerasifera accessions, those accessions were genotyped with a set of 24 common SSR markers, previously used in Armeniaca species (Liu et al, 2019. https://doi.org/10.15454/560LSH). The dataset was used to infer the relationship of P. brigantina (Briançon plum or Briançon apricot) with Armeniaca (apricot) and Prunus (plums) species, based on microsatellite markers and approximate Bayesian computation.