The number of hybrids has been reported to be lower in tropical than temperate ferns, but patterns of hybridization are poorly known in the tropics. We examine hybridization in the Neotropical fern genus Danaea (Marattiaceae) using a phylogenomic approach with single or low-copy nuclear and chloroplast loci and haplotype phasing. We find a high hybridization rate of 10%–18% for Danaea, similar to the rates observed for temperate ferns. We find further evidence for the previously proposed low reproductive barriers in ferns, enabling hybridization and even the production of hybridization-derived species between lineages separated possibly as far back as the Cretaceous. We found that Danaea trifoliata and D. wendlandii are fertile, hybridization-derived species between lineages diverged potentially 14–72 million years ago (mya) and 23–62 mya, respectively. We also confirm that the previously recognized species D. ×ushana is a likely sterile hybrid between D. simplicifolia (D. subg. Arthrodanaea) and D. nigrescens (D. subg. Danaea), which diverged potentially 27–83 mya. We find that hybridization may function as a homogenizing force in Danaea, as the subgenus with the highest signals for hybridization (D. subg. Arthrodanaea) also has the fewest species that are the least morphologically and genetically diverged. We describe a new hybrid between D. wendlandii (D. subg. Holodanaea) and D. subg. Danaea as D. ×deltoidea.