Pleopeltis polypodioides is a widespread Neotropical epiphytic fern consisting of six varieties and one subspecies. Objectives of this study were to assess placement of Polypodium polypodioides within the genus Pleopeltis, the monophyly of Pl. polypodioides, and the relationships and geographic patterns among its infraspecific taxa. Two plastid DNA regions (trnL_UAA-trnF_GAA and psbA-trnH_GUG) were sequenced for individuals across Pl. polypodioides geographic range. Maximum parsimony, maximum likelihood, and network analysis of cpDNA sequences were performed revealing evidence for seven haplotype lineages. The seven lineages, based on sister relationships, can be reduced to four clades within the Pleopeltis polypodioides complex, each of which have distinctive geographic ranges. Clade 1 (Pl. p. vars. burchellii and polypodioides) was found primarily in South America and the Caribbean basin. Clade 2 (Pl. p. subsp. ecklonii) is restricted to southern Africa. Clade 3 (Pl. p. vars. knoblochianum and acicularis) was found only in the north and western regions of Mexico. Clade 4 (Pl. p. vars. acicularis and michauxiana) extends from northeastern and southern Mexico into the U. S. A. and the northern Bahaman Archipelago. Analyses of the data did not fully support the monophyly of Pl. polypodioides; however the majority of the recovered clades correspond to currently defined taxa. Our analyses is of special interest in that it takes a population level approach to a molecular phylogenetic study and provides clarity to a taxonomic group that has proved difficult to elucidate. The results have added to a growing body of evidence that suggests Pl. polypodioides may consist of more than one species.