Orangutans (Pongo spp.) occur at low densities and therefore large areas are necessary to sustain viable metapopulations, defined here as sets of conspecific units of individuals linked by dispersal. Historically, orangutans lived in large contiguous areas of intact rainforest, but are now increasingly found in agricultural and other landscapes modified by people. Here we collate evidence of orangutans utilizing isolated forest fragments (< 500 ha) within multiple-use landscapes dominated by oil palm monoculture across Borneo. Orangutan signs (i.e. nests) were evident in 76 fragments surveyed by helicopter, and in 50 of 70 additional fragments surveyed on the ground; on average 63 ha in size. This includes presence of adult resident females with dependent young confirmed in 40% of the fragments assessed by ground survey. Our study revealed some resident females are raising offspring in isolated forest patches within mature oil palm stands. This not only confirms that some forest patches can sustain orangutans, but indicates migratory males are capable of reaching these fragments scattered throughout the multiple-use landscape. Therefore, orangutans that use or live in even small isolated forest patches are an essential part of the overall metapopulation by maintaining gene flow between, and genetic connectivity within, populations distributed across larger multiple-use landscapes. Orangutan survival is commonly thought to be low in small, isolated forest patches, and the customary management strategy is to remove (translocate) these individuals and release them in larger forests. In some cases, translocations may be necessary, i.e. in case of fire or when the animals are in eminent danger of being killed and have no other refuge. However, the small amount of data available indicates that mortality rates during and after translocations are high, while the impacts of removing animals from spatially dispersed metapopulations are unknown. Therefore, we argue the current policy of routine translocation rather than conserving the species within human-modified landscapes could inadvertently decrease critical metapopulation functionality necessary for long-term viability. It is clear that orangutans need natural forest to survive, but our findings show that fragmented agricultural landscapes can also serve as complementary conservation areas in addition to fully protected areas if they are well designed with ecological connections, and if orangutan killing can be prevented. To achieve this, we call for a paradigm shift from the traditional large single forest model to one that emphasizes metapopulation functionality in the fragmented foresthuman use matrix characteristic of the Anthropocene.