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In the Alhambra (Granada, Spain), and in other Moorish locations, several individuals of the original variety of myrtle, the emblematic plant of their gardens, have been identified and genetically authenticated. After microsatellite analysis, we differentiated between the wild form (Myrtus communis L.) and two cultivated varieties: the one original to the Alhambra, the Moorish myrtle (subsp. baetica), and the variety introduced in more modern times (subsp. tarentina). The genetic and morphological differences between these two varieties confirm the taxonomic distinctness of the subsp. baetica. With very few individuals known, this Moorish myrtle is on the verge of extinction. The genetic identification offers the opportunity to restore a key element of this 14th-century garden and enhance the authenticity of a World Heritage site.