Herbaceous plants are often under-studied in tropical forests, despite their high density and diversity, and little is known about the factors that influence their distribution at microscales. In a 25-ha plot in lowland Amazonian rain forest in Yasuní National Park, Ecuador, we censused six species of Heliconia (Heliconiaceae) in a stratified random manner across three topographic habitat types. We observed distribution patterns consistent with habitat filtering. Overall, more individuals occurred in the valley (N = 979) and slope (N = 847) compared with the ridge (N = 571) habitat. At the species level, Heliconia stricta (N = 1135), H. spathocircinata (N = 309) and H. ortotricha (N = 36) all had higher abundance in the valley and slope than ridge. Further, H. vellerigera (N = 20) was completely absent from the ridge. Conversely, H. velutina (N = 903) was most common in the drier ridge habitat. The two most common species (H. stricta and H. velutina) had a reciprocal or negative co-occurrence pattern and occurred preferentially in valley versus ridge habitats. These results suggest that taxa within this family have different adaptations to the wetter valley versus the drier ridge and that habitat partitioning contributes to coexistence.