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In our research we examined the role of marginal (ecoton) ecosystems in the formation of biodiversity of islands or isolated territories which could be considered as “islands”. The goal was to evaluate the ecological-coenotic composition of the flora of coastal or marginal vegetation communities and to identify the strategy of flora conservation on the islands. The investigations were made in the Chinese island Hainan and mountain forests of southern Kazakhstan (Karkaralinskie mountains) isolated from other forests by vast territories of steppe zone. Research works were made in 2008-2010 years. For each type of island we identified the sites more favorable as retreats for plants and studied the border communities of the whole island. For Kazakhstan mountain forests we showed that ecoton communities are more diverse than inner communities as for ecological-coenotic groups and in floristic composition. For coastal communities of Hainan island we showed that floristic composition is poor and flora of coastal communities is composed by pioneer or ruderal plants common for most coastal communities of tropical islands. For all island and “island” communities we showed that certain habitats, such as springs, banks of small brooks, valleys of temporal currents, lakesides, quagmires, bogs, cracks in the mountain blocks, submontane niches are favorable for preservation of rare species. For each type of island we revealed the rare species. For Kazakhstan mountain forests they are such species as Althaea officinalis, Berberis karkaralensis, Anemone coerulea, Neottia camtschatea, Gymnocarpium robertianum, Gymnocarpium dryopteris, Lonicera pallasii, Hypericum perfoliatum, Dracocephalum peregrinum, Saxifraga sibirica, Nymphaea candida, Papaver tennelum, Epipogium aphyllum, Moneses uniflora, Artemisia glabella, Coridalis schanginii, Dictamnus angustifolius, Dactylorhiza fuchsii. For Hainan island some rare species are Liquidambar formosana, Kleinhovia hospida, Spondias pinnata, Tilia hainanensis, Meyna hainanensis, Hopea hainanensis. Thus, islands can provide habitats for conservation of rare plant species while marginal or ecoton communities can serve as buffer zone between these refuges and surrounding ecosystems. The results of this work can be used for organization of natural reserves on the islands or isolated territories.