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Alternative berry crops belonging with the Rosaceae family currently have a great importance in the US and Canadian agribusiness, in this sense, the Mexican serviceberry (Malacomeles denticulata) is a fruit shrub mainly distributed in Mexico that has potential uses like horticultural crop; however, little information about its variability has been reported. That is why this research aims to determine the variability of M. denticulata by SSR markers. The apple SSR markers had a good transferability to Malacomeles (74 %); all transferable SSR are polymorphic and sixteen of them had high values of polymorphic information content, Nei’s expected heterozygosity (He), and Shannon’s information index (I), even the apple SSR loci were not previously proved in this species. Besides it was found high variability in the germplasm of central Mexico mainly within populations (72 %), where three different genetic pool were detected suggesting that a breeding program could be based in individual selection. That is why it is necessary select outstanding individual into population before to make hybridizations among these selected parents.