The origin of ×Lindsaeosoria flynnii as an intergeneric hybrid between Lindsaea ensifolia and Odontosoria chinensis is here confirmed by molecular analysis of plastid data and Illumina high-throughput sequencing of the low-copy nuclear LEAFY gene. Plastid DNA grouped the hybrid together with Lindsaea ensifolia, suggesting that it is the maternal progenitor, while the presence of distinct LEAFY alleles confirmed the hybrid origin. Together with ×Cystocarpium this is confirmed example of deep hybridization event between fern lineages that were separated in the early Cenozoic or late Mesozoic.