Evidence for a southern South American lineage of polygrammoid ferns was inferred from analyses using four cpDNA markers. The lineage corresponds to the genus Synammia, which has usually been treated as a synonym of the polyphyletic genus Polypodium. Seven specimens of two of the three recognized species were sampled to infer the phylogenetic relationships of this lineage to other polygrammoid ferns and the diversity within this lineage. All approaches found Synammia clearly separated from other polygrammoid ferns, but the exact relationships are still unclear. Model-based methods recovered Synammia as sister to a mainly Neotropical clade of polygrammoid ferns, but support for this hypothesis was provided only by Bayesian inference of phylogeny. The deletion of nearly the whole rps4-trnS IGS is a synapomorphy of Synammia. The lineage is separated from other extant polygrammoid ferns, but very low to zero sequence diversity was found among the seven samples of Synammia. The results strongly support an independent lineage of polygrammoid ferns in southern South America.