We investigated microhabitat selection in the Amazonian whip spider Heterophrynus longicornis (Butler 1973). The probability of finding individuals of this species increased according to the diameter of the trees. Moreover, there was a positive correlation between the size of adult individuals and the diameter of the trees on which they were found. Our results also provide quantitative support for a previous suggestion that H. longicornis prefers large trees bearing buttresses and burrows at the base where the individuals hide during daytime. Since whip spiders prefer large trees, the anthropogenic disturbance promoted by selective logging or the degeneration of the forest structure due to fragmentation and edge effect may have a negative effect on the spatial distribution and, consequently, on the density and population ecology of H. longicornis.