The market demand for interesting varieties and cultivars of Ilex aquifolium necessitates the exploration and sustainable exploitation of plant individuals thriving in nature without human care. In this work, an effort was made to develop a simple and reliable protocol for vegetative propagation of I. aquifolium plants, with desirable-for-market characteristics, grown in a mountain area of Halkidiki, Greece, and at the same time to proceed with their genetic identification using molecular markers. From these plants, new plants were vegetatively produced which afterward were used as stock plants for providing the needed shoot cuttings for the experiments of rooting and leaves for their genetic analysis. Factors studied in formulating a propagation protocol included the season of cutting collection and the application of 0.2% 1-naphthaleneacetic acid (NAA), as well as the type of shoot cuttings (terminal, subterminal) and the application of auxin. It was found that application of NAA was crucial for rooting response and number of roots formed, whereas the season effect was not significant on rooting. Terminal cuttings treated with 0.2% NAA exhibited the highest rooting percentage (100%) and formed abundant roots (25.7) compared to subterminal ones. All rooted cuttings, after being potted and transferred to acclimatization greenhouse, were successfully hardened. In the spring of the next year, the produced plants blossomed abundantly and formed fruits (bright red berries) presenting their characteristic ornamental appearance that was maintained until Christmas. For the identification procedure, the genotypic profile of the stock plants was also investigated by inter-simple sequence repeat (ISSR) genetic analysis, revealing that they were genetically the same both among themselves and when compared with a certified I. aquifolium ‘Agrifoglio Commune’ individual, but they differed genetically from I. aquifolium ‘Argentea Marginata’ and I. aquifolium ‘Hellas’.