The Junin giant frog Telmatobius macrostomus (Peters, 1873) is an Endangered and endemic frog in the central Andes of Peru. However, no quantitative ecological data exist to facilitate characterization of T. macrostomus habitat, nor do estimates of occupancy and detection probability, all of which are vital to inform appropriate management decisions. We present novel data on the current distribution and habitat of T. macrostomus in 3 natural protected areas in the regions of Junin and Pasco, Peru. To provide a general description of the areas where T. macrostomus occurred and did not occur, we measured a variety of physical, chemical, and biological conditions. We found T. macrostomus in fewer than half the streams surveyed for an estimated occupancy and detection probability of 0.40 +/- 0.11 SE and 0.84 +/- 0.06 SE, respectively. Akaike's information criterion (AIC) indicates that of the 20 single-variable models constructed during this study, 5 were substantially associated with T. macrostomus occurrence (Delta corrected AIC [Delta AICc] < 2). The % Chironomidae metric of benthic macroinvertebrate communities at sampled sites best predicted the occurrence of T. macrostomus, followed by pH. Specific conductance, % silt and rainbow trout Oncorhynchus mykiss were also associated with T. macrostomus occurrence. Although the most parsimonious multi-variable occupancy model only included % Chironomidae, pH and rainbow trout as predictive variables of T. macrostomus occurrence, the other single-variable models with apparent influence over T. macrostomus occurrence may also be used to identify adequate areas for Junin giant frog conservation.