The rhizomes of all species in the fern genus Lecanopteris Reinw. contain galleries (hollow chambers) that serve as domatia (homes) for ants. Some aspects of the biology of these species have been elucidated clearly, e.g., adaptations linked to the facultative, co-ecological association between Lecanopteris species and ants have been well established. Other aspects such as the evolutionary relationships between Lecanopteris and other genera of the Polypodiaceae as well as among the thirteen species in Lecanopteris remain widely debated. Diverse leaf and rhizome features have provided numerous autapomorphic characters for diagnosing species and describing subgenera, but there are few synapomorphies to establish reliable interspecific alliances. DNA sequences of the rbcL gene and the trnL-F non-coding region were obtained to test hypotheses of evolutionary history for Lecanopteris and related taxa. Data from each DNA region were considered separately and in combined analyses. The phylogeny obtained from parsimony and maximum likelihood analyses of separate and combined data sets were congruent, but the analyses of combined data sets contained more informative characters, more robust bootstrap support, and better Bremer (“decay”) values than did analyses of the individual DNA regions. Lecanopteris was solidly supported as monophyletic, subgenus Lecanopteris appeared monophyletic, but subgenus Myrmecopteris was paraphyletic. Rhizome morphology, including surface indument, branching patterns, and internal galleries, correlated with DNA-based hypotheses of evolutionary history and interspecific relationships, but aspects of leaf morphology, including blade shape and soral position, appeared homoplastic. Low levels of infrageneric sequence divergence between morphologically distinct species suggest a relaxation of selective pressure on morphology, perhaps owing to the ant/plant association. Narrowly distributed, derived species may have arisen as peripheral isolates from more geographically widespread progenitors.