The phylogenetic position of the monotypic genus Kontumia (Polypodiaceae) is contentious. It has been suggested that Kontumia is related to Gymnogrammitis dareiformis (Drynarioideae) based on spore ornamentation and blade dissection, or it has been assigned as a member of microsoroid ferns (Microsoroideae) based on the shape of rhizome scales. In the present study, we determined the phylogenetic position of K. heterophylla using four chloroplast DNA regions (rbcL, atpB, rps4 + rps4-trnS intergenic spacer [IGS], and trnL-F IGS). A parsimony consensus tree indicated that K. heterophylla is not related to G. dareiformis, but is nested within the Leptochilus lineage of Microsoroideae. This relationship is also supported by sharing of clathrate scales on the rhizome, which is not found in G. dareiformis. Although marked morphological disparities are found between K. heterophylla and the Leptochilus lineage in terms of leaf dissection, fertile-sterile leaf differentiation, and sori arrangement, our results indicate that these characters have evolved independently several times in Polypodiaceae.