Green Iguanas (Iguana iguana) are invasive in Puerto Rico due to a variety of negative economic effects, yet we know very little about their ecological impacts. Because they are herbivorous, defecate intact seeds, move through the forest, and have long gut-passage times, Green Iguanas may affect seed germination and seed dispersal. In summer 2013, a total of 258 Green Iguana scat samples were collected at the Humacao Natural Reserve in southeastern Puerto Rico. Seeds extracted from scat and collected from fruit were planted under common garden conditions using experimental treatments designed to tease apart the effects of feces, fruit, and ingestion on seed germination. Green Iguanas decreased the time for seeds to germinate in Ficus spp. by removing fruit pulp, but had no effect on germination of native Annona glabra seeds. For nonnative P. pterocarpus and Pterocarpus spp., Green Iguanas produced conflicting results, decreasing the percentage of seeds germinating, but at the same time, reducing the time for seeds to germinate. Green Iguanas likely disperse most seeds beyond the canopies of parental tree at our site. Government and economic resources are being used to eradicate Green Iguana populations in Puerto Rico, but the lack of consistent effects of Green Iguanas on seed germination for the plant species consumed at our site complicates generalizing about their ecological effects and developing management plans that minimize negative effects for native plant communities. We recommend additional studies that target both species of particular concern, such as threatened native or invasive species, as well as studies of sensitive habitats in Puerto Rico.