Compared to traditionally used plastid or ribosomal markers, nuclear gene markers provide many advantages for molecular systematics of plants, and high-throughput sequencing technologies are making large nuclear datasets available at an unprecedented rate. We used targeted amplicon sequencing of 44 nuclear genes to construct a time-calibrated phylogeny of genus Metrosideros (Myrtaceae), evaluate recent systematic revisions, and assess whether phylogenetic signal within the Hawaiian Archipelago is correlated with island biogeography or morphological diversification. We generated a final dataset of 40 nuclear genes for 187 specimens, used multiple search heuristics and species-tree analysis to estimate a phylogeny, and incorporated new fossils for the genus to estimate divergence times across the dataset. All analyses supported the monophyly of Metrosideros, including Carpolepis and Tepualia. Hawaiian Metrosideros were monophyletic and dated to 3.1 MYA using new fossils for the genus, which is intermediate to previous estimates based on nuclear ribosomal/chloroplast loci and calibrated with island ages. Within the Hawaiian Metrosideros clade, we observed short branch lengths and unresolved relationships, and phylogenetic patterns were not concordant with biogeographic hypotheses of island progression, or the delineation of taxa or morphotypes. Average nucleotide diversity was relatively consistent across the Hawaiian Islands with the exception of slightly lower diversity on Kaua'i. These results provide a data-rich estimate of the timing of a single introduction of Metrosideros to Hawai'i and highlight the need for molecular markers with higher evolutionary rates for resolution of relationships within this recent radiation.