The Moorea Biocode seeks to compile an integrative taxonomy based on morphological, ecological, and molecular data for the entire macrobiota of the island of Moorea, French Polynesia. As a case study exploring the utility of selected molecular data for species identification within this integrative taxonomic framework, chloroplast DNA from three regions (rbcL, trnSGG, trnH–psbA) were sequenced for all species of filmy ferns (Hymenophyllaceae) known from Moorea. The relative utility of each of these regions for the purposes of phylogenetic analysis and DNA-based identification was inferred by estimating support for phylogenetic trees reconstructed from each region and by calculating intraspecific and interspecific distance values (uncorrected p) between taxa for each region. All three of these regions were found to be potentially useful for phylogenetic studies at the appropriate taxonomic level. trnH–psbA was determined to have the greatest utility as a potential marker for DNA-based identification because of its high interspecific variability and high degree of amplification success. rbcL and trnH–psbA were successfully used in combination with morphological characters to identify a previously unidentified Moorean filmy fern species, Polyphlebium borbonicum. The presented results support trnH–psbA as appropriate for completing the plant section of the Moorea Biocode, although the use of additional markers will be necessary.