Amazonia is one of the world's leading suppliers of timber and the Amazonian timber industry is an important source of regional income, however the economic benefits of this market are associated with environmental damage, mainly when the wood is removed illegally. The Anavilhanas National Park, located in the Brazilian state of Amazonas, has been subjected to illegal logging and elaboration of control programmes requires knowledge of the distribution of timber species and the intensity of logging. This study examines the density and growth rate of the five most harvested tree species in the Park, the spatial distribution of illegal logging operations and their effects on population structure. In total, 2332 trees with diameter at breast height greater than 10 cm, as well as stumps of cut trees, were sampled, and dendrochronology was used to estimate growth rates. Some size classes of Virola surinamensis trees and species within the family Lauraceae decreased in abundance as harvesting intensity increased. Growth rates of the most abundant species of Lauraceae, Ocotea cymbarum, were high, indicating stands may recover quickly when harvesting stops. The population structure of Calophyllum brasiliense showed no negative effects due to logging, but its low growth rate and stand distribution suggest that continued exploitation may endanger these populations. Logging had no detectable negative effects on the size structure of populations of Macrolobium acaciifolium or Hevea spp., and their high growth rates suggest that they will not be threatened by current logging rates. Overall growth rates in the Anavilhanas archipelago are higher than those recorded in other black-water floodplain forest (igapó). Logging of most species (except Lauraceae spp., which have the highest market value) is concentrated in the southern region of the Park, which has more human settlements close by. There was no general relationship between harvesting intensity and geographic distance to human settlements, but there was a tendency for harvesting to be higher in sites with concentrations of trees of high market value. Potential strategies to control illegal logging activities in the Anavilhanas archipelago include encouragement of sustainable logging in Park buffer zones and stimulation of ecotourism initiatives in the southern region of the Park. Ecotourism development can provide an economic alternative to illegal logging for local communities and inhibit logging by increasing vigilance.