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Davallia repens and its close relatives have been identified as a species complex in this study because of the existence of continuously morphological variation. To decipher its evolutionary history, integrated methodologies were applied in this study including morphology, cytology, reproductive biology and molecular phylogeny. Analysis of morphological characters reveals several important discriminating characteristics, such as the shape of stipe scales, frond and indusium. Both diploid and polyploid forms are present in the complex and reproduce sexually and by apogamy, respectively. The incongruence between cpDNA and nDNA phylogeny indicates a hybrid origin for most polyploid individuals. Based on the present results, we hypothesize that there were at least two ancestral lineages distributed in the Malesian region. Through hybridization, polyploidization and apogamy, some polyploid genotypes dispersed outwards to shape the extant distribution.