Amphibian populations are declining due to a myriad of abiotic and biotic factors, including invasive species and pathogens. In temperate freshwater ecosystems, for example, amphibian populations are threatened by the predation of introduced salmonids. Salmonids not only directly predate upon amphibian eggs and larvae but may also transport deadly pathogens into freshwater systems. Though most research has focused on temperate systems, much less is known about the effects of introduced species in Neotropical streams. We conducted two experiments to investigate the impacts of rainbow trout (Oncorhynchus mykiss) in two Neotropical anurans. First, we assessed the effect of the rainbow trout on tadpole survivorship and morphology in Nymphargus grandisonae, a glassfrog species endemic of the Andes. Tadpoles of N. grandisonae were subjected to three treatments involving the absence of rainbow trout (control) and its presence with different types of chemical cues–kairomones (from rainbow trout) and cue alarms (from tadpole prey); the results show that the presence of rainbow trout affects the larval morphology of this glassfrog. In the second experiment, to test whether rainbow trout is a vector of the pathogenic freshwater mold Saprolegnia diclina (Oomycetes), eggs of Engystomops petersi were placed with infected and uninfected rainbow trout. There was a high mortality rate in the embryos of E. petersi exposed to trout infected with S. diclina. This represents the first evidence that rainbow trout may have a direct negative effect on Neotropical amphibian populations, and thus should be considered a threat. Management programs should be implemented to eradicate trout from Andean rivers, especially in areas with high number of endangered amphibians.