We report results of an ichthyological survey of the Lower Urubamba river, a tributary of the Ucayali river located in the southwestern portion of the Amazon Basin in southeastern Peru. Collections were made at low water (July, 2009) from 280 - 310 m elevation, near the town of Sepahua within the Fitzcarrald Arch, an upland associated with Pliocene (c. 4 Ma) uplift of the Peruvian Andes. This is the second of four planned expeditions to the region with the goal of comparing ichthyofaunas across the headwaters of the largest tributary basins in the western Amazon (Juruá, Ucayali, Purús and Madre de Dios). Twenty-one sites were sampled using seine nets, hook lines, cast nets and dip nets. A total of 98 species in 22 families and eight orders were captured and identified. The most diverse families are Characidae (40 spp.) and Loricariidae (20 spp.), and 12 families are represented by a single species. These data suggest that the fish fauna of the Lower Urubamba river near Sepahua is distinct from, and less diverse than, adjacent areas of lowland Amazonia.