The capacity for flight varies widely among bird species and influences their ecology, evolution, and conservation. Variation in vagility is influenced by behavioral responses to the nature of gaps between habitat elements as well as intrinsic characteristics of the species, particularly physiological traits influencing the physical capacity for sustained flight. Here, we briefly summarize the current state of knowledge revealing the wide variety of movement capacities of Neotropical birds. We then review current knowledge of avian muscle physiology and the role that muscle characteristics may play in influencing movement behavior. We argue that fundamental shifts in our understanding of avian muscle physiology and the influence of physiology on movement behavior remain to be elucidated, in part because knowledge from other vertebrates is being inappropriately applied to birds. In particular, critical evaluation of assumptions applied to birds from detailed studies of mammals is needed. Moving away from simple binary categorizations of avian flight muscles as “red vs. white” or “fast vs. slow” to characterize the cellular mechanisms and specific isoforms active at various life stages or seasons is also needed. An increasingly large number of avian species with a wide array of flight styles from hummingbirds to soaring raptors are appearing in GenBank, facilitating detailed physiological and evolutionary comparisons among species. Properly assessing the muscle physiological characteristics of Neotropical bird species with a wide array of movement capacities may improve our abilities to predict which species are most sensitive to landscape fragmentation and other factors that influence dispersal and migration.