Habitat preferences and response to habitat conversion remain under-studied for many groups in the tropics, limiting our understanding of how environmental and anthropogenic factors may interact to shape patterns of diversity. To help fill this knowledge gap, we surveyed nocturnal birds such as owls, nightjars and potoos through auditory transect surveys in 22 forest fragments (2.7 to 33.6 ha) in north-west Ecuador. We assessed the relative effect of habitat characteristics (e.g. canopy height and openness, and density of large trees) and fragment attributes (e.g. area, altitude and proportion of surrounding forest cover) on species richness and community composition. Based on our previous work, we predicted that nocturnal bird richness would be highest in relatively larger fragments with more surrounding forest cover. We recorded 11 total species with an average ± SD of 3.4 ± 1.4 (range = 2–7) species per fragment, with higher richness in fragments that were larger, at lower altitudes, and characterized by more open canopies. Nocturnal bird community similarity was not significantly correlated with any measured environmental variable. These results indicate that both landscape (e.g. altitude) and fragment-specific (e.g. size, forest structure) attributes are likely to interact to shape patterns of diversity among this poorly known but ecologically important guild in fragmented tropical landscapes.