This dissertation deals with the systematics and evolution of Neotropical ferns of the genera Elaphoglossum and Asplenium, with particular focus on the species of Cuba and the West Indies. It also includes an analysis and description of an Elaphoglossum frond fragment preserved in Miocene Dominican amber. The worldwide genera Elaphoglossum with 600 species and Asplenium with 685 species are the most species-rich groups of leptosporangiate ferns. On Cuba, Elaphoglossum has 34 species and Asplenium 32. I performed phylogenetic analyses of plastid DNA sequence matrices that included almost 300 sequences of Elaphoglossum and its closest outgroups, with especially dense sampling of the Cuban Elaphoglossum, mostly newly sequenced during my research. The Cuban endemic E. wrightii was found to be an early-diverging lineage of Elaphoglossum, not a member of section Squamipedia in which it had previously been classified; I, therefore, created a separate section for this species. This species climbs upwards on the lower portions of tree trunks but never loses its connection with the soil while most remaining species of Elaphoglossum retain no connection to the soil and are holo-epiphytes. The plastid DNA phylogeny in combination with an in-depth analysis of the morphology of West Indian Elaphoglossum allowed me to confidently assign a fern inclusion from Miocene Dominican amber to the genus by reconstructing the evolution of relevant morphological characters (preserved in the fossil) on the molecular phylogeny of extant taxa. The infrageneric classification of Asplenium is notoriously difficult as a result of extensive morphological homoplasy and plasticity. Molecular-phylogenetic studies have shed light on major lineages within Asplenium including some morphologically highly distinct species. Among these is Asplenium nigripes, a species occurring in Costa Rica, Guatemala, and Cuba where it grows on rocks in mountain forests between 900 and 1500 m. The species is unusual in having entire suborbicular to rhomboid fleshy blades that do not look like typical fern fronds. My molecular phylogenetic analysis revealed that it is the sister species to A. pumilum, also occurring on Cuba but with ‘normal’ fern leaves except for unusual whitish hairs. Using micro-morphological leaf and spore traits, I tried to find additional support for a close relationship of these two species, but was unable to detect any synapomorphies, which highlights both the importance of molecular characters for investigating species relationships in Asplenium and our still incomplete knowledge of the phenotypic traits of Cuban ferns.