The taxonomic identity and the geographical relationships of the Macaronesian endemic moss Fissidens luisieri have been studied using the chloroplast trnG_UCC intron, the spacer between trnM and trnV, together with the trnV intron and ITS1 and ITS2 sequences. A comparison of F. luisieri with the most closely related species, F. serrulatus, from the same geographical areas reveals that the distribution pattern of F. serrulatus and F. luisieri, rather than their morphological differences, explains the observed differences. Therefore, we conclude that both names correspond to the same species. One of the primers for the chloroplast trnG_UCC intron and both primers for the trnM–trnV region were designed for this study; they can all be widely used within bryophytes because they provide similar degrees of variability as other regions of the chloroplast genome such as the atpB–rbcL intergenic spacer.