Across vertebrates, there is a broad correlation between neuroanatomy and the type of habitat preferred by a species. In general, species occupying habitats classified as more structurally complex have relatively larger brains and exaggerated structures related to navigating and exploiting those habitats. We empirically measured the structural habitat complexity of six species of Puerto Rican Anolis lizards, which have traditionally been classified as occupying three distinct habitat types. We also measured the volume of the whole brain as well as six structures putatively related to exploiting complex habitats in these species. We found a significant interspecific variation in structural habitat complexity, including a substantial variation between those belonging to the same ecomorph category. Despite this, we found no evidence to support the hypothesis that interspecific differences in habitat preferences, particularly differences in the relative structural complexity of those habitats, can favor a divergence in neuroanatomy. However, our findings indicate that, at a finer scale, species preferences for structural habitats vary greatly between Anolis species belonging to the same ecomorph category. This variation might contribute to the community structure of anoles by allowing multiple sympatric species of the same ecomorph category to occupy what, at a coarse scale, appears to be the same structural niche. We propose that, in the case of arboreal species, differences in the complexity of arboreal habitats alone may not be sufficient to favor divergent brain evolution.