This paper describes experience gathered in Central Europe, regarding the sometimes problematic side-by-side existence of native forest tree species and closely related introduced plantation species, varieties, and clones. The main focus will be the conservation of genetic diversity of native species, that is, how to maintain gene pools that are large enough and of adequate composition, in order to ensure the future survival of the species in all the ecosystems it is currently associated with. Two examples are given: black poplar (Populus nigra L., hei yang) is a floodplain forest pioneer species which is affected by cultivation of clones in great numbers, mainly of hybrid origin. The common yew (Taxus baccata, hongdoushan) is an understory, late-succession species throughout much of Europe, which is potentially affected by horticultural varieties. Through their contrasting life-history traits, they serve well to deduce general principles and recommendations for genetic conservation in tree species in similar situations. The main conclusion from these examples is that each case requires careful consideration based on the specific biological, ecological, geographical and management cirucumstances.