Understanding the evolutionary relationships of threatened species provides an important framework for making decisions about their conservation. However, unrecognised problems with the underlying phylogenetic analyses may bias the decision-making process. Recent phylogenetic studies have improved our understanding of Meliphagidae, but also indicate discordance between molecular datasets. Here, we examine the causes of this discordance using maximum likelihood tree-building and network analyses of identically sampled datasets for four genetic loci. Our results suggest that while we can be reasonably confident of relationships within species groups, discordance within and between molecular datasets tends to obscure relationships towards the base of the meliphagid tree. This ongoing uncertainty likely reflects differences in the sampling of markers and taxa between previously published analyses. To avoid the problems of conflicting data we used divergence time analyses of only the most densely sampled marker, NADH-ubiquinone oxidoreductase chain 2, to investigate the age and origins of the Fijian Meliphagidae. Our analyses suggest two temporally distinct colonisations of the Fijian archipelago. The large-bodied honeyeaters arrived ,15.6 million years ago, subsequently diversifying and spreading to Tonga and Samoa. In contrast, Myzomela appears to have arrived within the last 5.0 million years. The phylogenetic results therefore imply that conserving the evolutionary diversity of Meliphagidae in Polynesia requires that effort be spread across both the currently recognised taxa and geographical range.