The diversity and spatiotemporal variation of avifauna in different settings of tropical coral reef-karst forests on the Hengchun Peninsula, Taiwan, were examined. The short-term effects on bird assemblages following two typhoons that severely impacted Hengchun were investigated. Line-transect census recorded 46 species of birds, dominated by forest-associated gleaning insectivores or omnivores, and 13% of the endemics of Taiwan. Prior to the typhoons, the continuous-canopy forest was close to the open forest setting in species evenness, but the species heterogeneity was lower and more variable. The continuous-canopy and open forests differed in overall avian composition, whereas two continuous-canopy forest settings were similar in composition. Typhoons did not significantly lower the mean numbers of either species or birds, nor affect the pattern of their spatial distribution in the forest settings. However, they did increase similarities in the species composition between the open and continuous-canopy settings, and caused a decrease in the similarity between forest edges and interiors. Overall, typhoons affected species composition more in the continuous-canopy forests than in the open setting, and more in interiors than in forest edges. This pattern corresponded to an increase in the species heterogeneity and species evenness in the forest interiors, indicating movements of birds from the edge toward the interior. Among different functional groups, gleaning omnivores tended to retain a pattern of higher abundance in the open forest setting than in the continuous-canopy forests, whereas the abundances of gleaning insectivores and cavity-nesting frugivores tended to decline in the latter or both settings.