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We examined the effects of selective timber logging carried out by local indigenous people in remote areas within indigenous territories on the mammal populations of the Yavari-Mirin River basin on the Peru-Brazil border. Recent findings show that habitat change in the study area is minimal, and any effect of logging activities on large mammal populations is highly likely to be the result of hunting associated with logging operations. We used hunting registers to estimate the monthly and yearly biomass extracted during timber operations and to calculate the catch per unit effort (CPUE) in subsistence hunting in the community of Esperanza 2 to 5 years before logging activities started and 4 to 7 years after logging began. We also used line transects and the distance method to estimate animal densities before and after logging. We found that 1389 hunted animals and 27,459 kg of mammal biomass were extracted per year from logging concessions. CPUE for ungulates declined; however, it increased for other mammal orders, such as rodents and primates, indicating a shift to alternative prey items. Although collared peccaries (Pecari tajacu) and tapirs (Tapirus terrestris) may also have declined in numbers, this shift may have been caused by a possibly natural population crash in white-lipped peccaries (Tayassu pecari) that coincided with the logging periods. We found no evidence that populations of primates were reduced by the logging activities. Because primates are sensitive to hunting, and their populations were of principal concern as logging commenced, this indicates that these forests remain of high conservation value. The unusual socioeconomic situation of these remote territories may mean that they are compatible with wildlife conservation in the Yavari-Mirin basin.