The present study investigated the hypothesis that several fern species occurring in Macaronesia and Atlantic Europe are relicts of the Miocene Paratethyan–Tethyan flora that survived in Macaronesia refugia. The hypothesis was tested by reconstructing the phylogenetic relationships of the derived fern Davallia canariensis, which is the only species of a mainly South-east Asian family, Davalliaceae, occurring naturally in Europe, Macaronesia and northern Africa. The dataset comprised a comprehensive taxonomic sampling of the family, with representatives of the five major lineages and ∼50–60% of the extant species diversity. For each species, we included two coding regions of the chloroplast genome, namely, atpB and rbcL. Diversification times were estimated considering previous estimates of the crown and stem group age as well as the fossil record of Davalliaceae. The results were consistent with the hypothesis, by recovering D. canariensis as the only extant member of an isolated lineage that has been separated from other crown group Davalliaceae since the Late Miocene. The obtained results are discussed in the context of the Messinian salinity crisis, evolution of epiphytic habit in ferns, and the generic classification of Davalliaceae.