People from every culture observe the natural world in detail and organise it into categories, and Western biology builds on this universal impulse towards classification. Here we provide a quantitative analysis of factors that shape folk and scientific classification of birds from areas associated with three indigenous languages (Anindilyakwa, Tlingit, and Zapotec). We find that traditional Linnaean taxonomies align better with folk categories than do modern phylogenetic classifications, which suggests that human perception is responsible in part for the correspondence between Linnaean and folk taxonomies. Perceptual similarity is difficult to measure at scale, but we use the recently released AVONET database to develop a proxy for the perceptual similarity between pairs of birds and find that traditional Linnaean taxonomies and perceptual similarity both independently predict folk categories. Our results therefore provide quantitative evidence for the view that perceptual similarity influences both scientific and folk classification.