We examined phylogeographic patterns and cryptic diversity within the royal flycatcher, Onychorhynchus coronatus (Aves: Onychorhynchidae), a widespread Neotropical lowland forest tyrant flycatcher. A phylogeny of the six recognized subspecies was constructed from mtDNA sequence data of the NADH dehydrogenase subunit two gene, using Bayesian Inference and Maximum Likelihood methods. Phylogenetic analyses revealed high levels of intraspecific divergence within O. coronatus, supporting the existence of at least six independent lineages. The phylogenetic results uncovered the following relationships: (O. c. swainsoni [Southern Atlantic Forest], (O. c. coronatus [western Amazonia], (O. c. castelnaui [eastern Amazonia], (O. c. mexicanus [Central America], (O. c. occidentalis [Tumbesian], O. c. fraterculus [extreme northwestern South America])))). Biogeographic and dating analyses suggest that vicariant and dispersal events acted across approximately six million years to influence lineage diversification within this genus. Some of those events include the formation of the Amazon River and its tributaries, Andean uplift, and climatically induced vegetational shifts. Phylogenetic and biogeographic analyses of O. coronatus lineages support a hypothesis of area relationships in which the first divergence event isolated the Southern Atlantic Forest from Amazonia during the Late Miocene/Early Pliocene. This event was followed by the split of western and eastern Amazonia at the Early/Late Pliocene, the divergence of cis- and trans-Andean lowland regions also at the Early/Late Pliocene, the split between Central America and the extreme northwestern South America/Tumbes at the Early/Middle Pleistocene, and the split between extreme northwestern South America and Tumbes at Middle/Late Pleistocene. Subsequent divergence of the southern and northern populations in the western and eastern Onychorhynchus lineages took place during the Pleistocene. Comparison of phylogenetic trees and patterns in Onychorhynchus with those from published work suggests that across large New World radiations such as the Suboscines, some co-distributed lineages began to diverge long before others, which exemplifies the complexity of their evolutionary history.