The data are derived from established microsatellite markers previously developed for apricot and related species. The abbreviations used follow the original nomenclature provided by the researchers who created and published these markers. The full list of corresponding references is provided in the Materials and Methods section of the manuscript. List of markers: AMPA101_1, AMPA101_2, AMPA119_1, AMPA119_2, UDAp-410_1, UDAp-410_2, UDAp-414_1, UDAp-414_2, UDP98-411_1, UDP98-411_2, UDP98-412_1, UDP98-412_2, UDAp-420_1, UDAp-420_2, UDP96001_1, UDP96001_2, UDP98406_1, UDP98406_2, UDP98-409_1, UDP98-409_2, pchgms5_1, pchgms5_2, ssrPACITA19_1, ssrPACITA19_2.