Wood density is expressed by the ratio between dry weight and fresh volume of a sample piece. The value of this measure is an important variable for assessing wood functional properties, successional stages and biomass/carbon stock estimates in different terrestrial ecosystems. Wood density data were collected for tree species from ecotone forests of the northern Brazilian Amazonia. We sampled 680 individuals with stem diameter ≥10 cm. For each sampled individual measurements were taken for three stem variables: bark thickness (mm), bark density (g cm−3) and wood density (g cm−3). This dataset is intended to improve biomass and carbon estimates of forests in the northern ecotone region of Brazilian Amazonia, an area poorly known in terms of ecosystem dynamics.