Ferns and lycophytes are unique among land plants for having two morphologically distinct lifestages that can grow independently of each other for most of the life cycle. The vast majority of our knowledge of fern ecology is based on observations of the more obvious lifestage, the sporophyte. The ecology of fern gametophytes, in comparison, has been literally overlooked due to their small size and cryptic morphology. DNA barcoding—the identification of species using a standard segment of DNA—is a powerful tool that has the capacity to revolutionize our understanding of fern gametophyte ecology by enabling accurate identification of nearly any individual collected in the field. In this talk, I will review the field of DNA barcoding as applied to fern gametophytes, from initial proof-of-concept studies, to its current application using a set of standard markers obtained through Sanger DNA sequencing, to the exciting future that awaits to be unlocked by next-generation DNA sequencing technologies.