Epidendrum (Orchidaceae) has been suggested to be a promising model system for evolutionary and ecological studies in the Neotropical region. Given its species diversity, the broad biogeographical and ecological range, and the variation in morphology, chromosome numbers and ecological interactions, the genus presents a rich source for intriguing and yet unanswered questions. Epidendrum is also a prime candidate to study speciation and this makes establishing precise species boundaries and diversity estimates in the genus extremely important. Through the recognition and discovery of hundreds of undescribed taxa, the number of formally described Epidendrum species has grown from 1000 to 1800 in the last two decades, while projections suggest the genus may have up to ca. 2400 species. This notorious underestimation of species diversity has serious consequences in many macroecological studies, including speciation, biogeographical patterns, diversification processes, and conservation priorities. Such a large number of unrecognized species in the genus has multiple unforeseen negative consequences and closing the gap between the described and projected diversity needs to become a priority. The isthmus of Costa Rica and Panama, one of the most biodiverse regions in the world, is also a center of diversity of Epidendrum. One out of every six species in the genus is present in the region and half of them are endemic. In the current paper, 20 new species are described from the isthmus and new records and exclusions are presented for both countries. Many of the newly recognized species had previously been included within broader circumscriptions of other taxa or had simply been misidentified. They represent a good example of how taxonomy can cause a sudden shift from a scenario where a few broadly distributed and unthreatened species become multiple potentially threatened species for which the population size, distribution and conservation status need to be urgently established. Epidendrum is the most specious orchid genus in Costa Rica and Panama, as well as most other Latin American countries, but species are poorly represented in herbaria and literature, and indetermination or incorrect determination of specimens is widespread. This results in a severe underestimation of Epidendrum species both in terms of species richness and their conservation priority levels.