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Ex situ conservation is a common strategy for the restoration of endangered species. Botanical gardens play an important role in the restoration of plants; however, hybridization could happen if transplantation is not considered carefully. Two naturally allopatric taxa Acer albopurpurascens and A. buergerianum var. formosanum, grown in the Taipei Botanical Garden, hybridized spontaneously. Hybridization was shown by the presence of intermediate phenotypes and genetic data. To confirm the direction of pollen flow, indirect evidence of maternally inherited chloroplast DNA indicated that A. buergerianum var. formosanum was the pollen receiver. The hybrids shared parts of ancestral genetic variations with their parents. Furthermore, several novel haplotypes that were slightly different from their parents were cloned, which revealed higher genetic diversity of the hybrid population than the parental populations. Such a phenomenon is called the rare allele phenomenon. In comparison with haplotypes of parents and hybrids, and according to the estimation of minimum recombination events and the likelihood ratio tests, the genetic variations were brought about by recombination events, such that the rare allele phenomenon might be related to the recombination. The hybridization that occurred in the botanical garden underscores the importance of spatial isolation when carrying out ex situ plantations. [ABSTRACT FROM AUTHOR]