Phylogenetic relationships between Trogoniformes and several other putative closely related groups of birds, based on complete cytochrome b and nearly complete 12S ribosomal RNA sequences, were studied. The taxa included trogons, owls, cuckoos, parrots, nightjars, hummingbirds, kingfishers, motmots, rollers, mousebirds, and woodpeckers. The group most commonly suggested as the nearest relative to trogons had been the coraciiforms (kingfishers, rollers, and allies) but this hypothesis was not supported. It appeared that Trogons are more closely related to mousebirds, parrots, and perhaps cuckoos than to coraciiforms. Conflicting results, however, prevented precise determination of higher-level phylogenetic affinities of trogons. A saturation analysis showed evident saturation in cytochrome b third positions and 12S loops. After saturated partitions were removed, the phylogeny supported the mousebirds (Coliiformes) as the sister taxon to trogons. Phylogenetic inconsistencies appeared to be attributable to an imbalance between the lengths of terminal and internodal branches. Apparently, the limited number of characters supporting internodal branches exemplifies a relatively rapid cladogenesis at an early period in the evolutionary history of these birds.