More than 90% of harlequin frog species ( Atelopus spp.), endemic to the Americas, are currently threatened with extinction. We report the discovery of the only currently known breeding population of the Critically Endangered A. varius in Costa Rica. This population was located in 2008 on a private property in Las Tablas Protected Zone near San Vito, Coto Brus at 1300 m elevation. Previously, the only known remaining/remnant population of this species and genus was a single location near Manuel Antonio, Puntarenas, Costa Rica, where two individuals were documented in 2004. Subsequent searches at this location have yielded no additional sightings. Delineating the spatial limits of this population, quantifying demographics and resource use, and implementing conservation actions are necessary to ensure persistence of this population. Conducting additional surveys in this region to ascertain occurrence of additional populations is warranted.