We present a checklist for reptiles and amphibians of the Reserva Extrativista do Rio Gregório, at the upper Juruá River basin, in the southwest Brazilian Amazonia. Using time-constrained searches, pitfall traps, vocalization, and accidental sightings, we recorded 84 species: 46 amphibians and 38 reptiles. Although analyses suggest still higher diversity, considering the short sampling time, relatively high species richness was documented, which reveals the relevance of this region for conservation. Species richness did not differ between upland and floodplain habitats. Species compositions were significant different between these habitat categories for amphibians and snakes, but not for lizards, suggesting some habitat preferences. Additionally, we found threatened and vulnerable species. We did not assess impacts of human activities on natural populations in RESEX do Rio Gregório, but since resident people have directly used natural resources (e.g. consuming turtles and modifying natural habitats), we recommend monitoring biodiversity to avoid negative impacts.