Ecological adaptation within islands may have figured prominently in the insular radiation of black flies (subgenus Inseliellum) in the Society Islands, French Polynesia. To aid in understanding the sequence of ecological shifts in this group, we have constructed a phylogeny using morphology, the cytochrome oxidase I (COI) gene, and the small ribosomal subunit (12S) gene. The strong influence of COI on the combined analysis tree was evident from its contribution to the partitioned Bremer support (62%). The net effect of including 12S was to reduce overall tree support. Different character sets resolved different portions of the combined analysis tree, with COI resolving recent lineages, 12S resolving basal relationships and morphology supporting the monophyly of taxa possessing reduced larval feeding fans (oviceps group). The Partitionâ Homogeneity and Kashino-Hasegawa tests indicated significant incongruence between morphological and mitochondrial data. The Templeton test revealed that morphology and the combined (COI+12S) mitochondrial data were incongruent. This conflict stems primarily from disagreement over the monophyly of taxa with highly reduced larval feeding fans. Either 1) convergence in a subset of morphological characters, 2) low phylogenetic signal among mitochondrial sequences, or 3) lineage sorting causing the mitochondrial data to track an incorrect evolutionary history, may be responsible.