Asplenium flabellifolium Cav. is a cytologically variable Australian and New Zealand fern. Here, we sequence chloroplast trnL-trnF and rps4-trnS from samples throughout its range to provide the first phylogeographic investigation of a fern common in both countries. Twenty-three haplotypes were detected, which formed six haplogroups in a network. Australian specimens were placed in all haplogroups. The placement of New Zealand haplotypes in five of the haplogroups suggests that this species has dispersed across the Tasman Sea at least five times. Sexually reproducing plants of lower ploidy, detected only in south-eastern Australia, contained haplotypes from the two haplogroups that are successive sisters to the remaining diversity in the phylogeny. This likely suggests that A. flabellifolium was originally a sexually reproducing species in south-eastern Australia and spread to the rest of its distribution where apomictic plants dominate. More than one haplogroup was detected in several areas across its distribution, suggesting that these areas were colonised several times. Other areas harboured several haplotypes from a single haplogroup or haplogroups not recovered elsewhere, indicating possible long-term persistence in these areas. Haplotypes and morphological features were not found to be exclusive to either breeding system or ploidy and no taxonomic revision is proposed.