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The endemic palm from the Canary Islands, Phoenix canariensis, is one of the most distinctive elements of the Canarian vegetation landscape, contributing to cultural, economic and environmental aspects. One of the main conservation problems facing this iconic palm is anthropogenic hybridization with other Phoenix species, particularly Phoenix dactylifera, which has been introduced extensively throughout its geographical range. Therefore, it is important to obtain a genetic tool that addresses different issues that may have an impact on the protection of P. canariensis, including ornamental applications and wild population conservation purposes. Our main goals were to detect a molecular tracer that could reliably distinguish between Phoenix canariensis and P. dactylifera in the Canary archipelago and to characterize the presence and extent of genetic hybridization events between the two species. We used 19 nuclear microsatellites and 1 chloroplast minisatellite set and analysed a large sample size (N = 433) of plants using both Bayesian methods and ordination techniques. Our data showed that a set of 13 nuclear markers revealed diagnostic alleles for P. canariensis, which were defined as the Canarian nuclear genotype (CNG). Moreover, P. canariensis exhibited an exclusive chlorotype of 266 bp that together with the GNC serve as an indicator of genetic purity in the Canarian palm. These markers are sufficient to detect any hybrid, even if it is not related to morphological differences. The occurrence of a considerable number of specimens with different degrees of hybridization is discussed in terms of the existence of different generations of hybrids and different types of crosses. Thus, the genetic tracers represent an invaluable tool to address any proposal for the genetic conservation of Phoenix canariensis. Full article