Base-line data were collected to examine the possible effects of the aquarium trade on Amazon fish populations in differentially-fished locations in the Departmento of Loreto, Peru. Fish abundance, species diversity (richness) and biomass were quantified at three locations with differential fishing pressure, including the Rio Nanay (high pressure), Rio Apayacu and Rio Arambassa (medium) and Rio Yanayacu -Pacaya-Samiria National Reserve (low). Seining results indicated that the location with the highest fishing pressure had reduced fish abundance, species diversity and biomass compared to the other locations. A similar trend was seen using minnow traps. There was no significant difference in abundance, diversity and biomass between the medium and low fishing pressure locations. Habitat differences (pH and conductivity) among the three locations accounted for <13% of the observed variation, and thus it seemed possible that some of the decline in the Rio Nanay location could be tentatively attributed to increased fishing pressure. Although effects of pollution and habitat alteration could not be ruled out, this is one of the first studies to provide quantitative data on the effect of the freshwater aquarium trade on wild fish populations. While results suggest success in the protection of fishes for the aquarium trade in Pacaya-Samiria National Reserve, it also may be sustainable to establish limited levels of fishing, as was found in the medium fishing pressure locations, in order to promote economic opportunities and incentives for habitat preservation for indigenous communities.