Systematic relationships among monarch flycatchers (genus Monarcha) are poorly understood despite dramatic patterns of morphological differentiation that have long attracted the attention of evolutionary biologists. With sequence data from the mitochondrial ND2 gene and Control Region, we produced a phylogenetic hypothesis for evolutionary relationships within Monarcha and among the biogeographically complex Solomon Island endemics. Outgroup analyses contradicted monophyly of the genus by imbedding a representative of the genus Clytorhynchus within one of two major clades recovered within Monarcha. These two monarch clades generally correspond with ecological and morphological distinctions, suggesting the genus may warrant revision pending the inclusion of taxa currently allied with Clytorhynchus (e.g., Neolalage spp.). Maximum likelihood reconstructions support monophyletic groupings of the two endemic Solomon Island monarch radiations, however, two currently recognized superspecies (Monarcha manadensis and M. melanopsis) were polyphyletic and paraphyletic, respectively. Interestingly, molecular and morphological differentiation were strikingly decoupled among several Solomon Island endemics and between migratory and non-migratory forms of Monarcha trivirgatus in eastern Australia, suggesting morphological evolution has masked the true history of speciation in these groups. This initial phylogeny provides a novel platform for ongoing exploration of the history underlying dramatic patterns of geographic variation among tropical Pacific flycatchers.