The Neotropical region, which contains Mesoamerican, Antillean and South American countries, is well-recognized for harboring high levels of species richness and endemism, and diverse ecoregions and climate zones. The vast majority of taxa and ecosystems in this region still remain understudied. There is a large potential for contributions in taxonomy and phylogeny, biogeography and evolution, broad-scale ecological processes, tropical ecology, plant-animal interactions, and freshwater ecology; as well as applied research directed toward conservation and management. Despite the great opportunities for ecological research in Latin American countries, international research efforts by Japanese ecologists have been mostly focused on other regions and biomes, likely for reasons that range from geographical distance to cultural differences and language barriers. The great cultural differences between Japan and Latin America can certainly represent one of the key challenges for effective communication and research collaboration. Here, we present some of the opportunities and challenges for doing ecological research in Latin America (from the perspective of two Latin American researchers based in Japan) and further discuss the importance of cultural awareness for international collaborations in the Neotropics.