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Abstract Aim We address questions about trans-Pacific distributions of marine organisms and the North Pacific Ocean as a centre of marine biodiversity through a phylogenetic and biogeographical study of a pan-Pacific genus of Northern Hemisphere smelts (Hypomesus, Pisces: Osmeridae). Location North Pacific Ocean. Methods Relationships of the five species of Hypomesus from throughout the North Pacific were reconstructed through maximum likelihood and Bayesian phylogenetic analyses of sequence data from two mitochondrial (cytb, 16S) and three nuclear (ITS2, S71, RAG1) gene regions of five to 25 individuals per species, totalling 3588 characters. The resulting phylogenies were used to test hypotheses of species relationships and geographical origins using both dispersal-based and maximum likelihood methods for inferring ancestral areas (lagrange). Cytb sequence divergence and a Bayesian approach (beast) were used to estimate the timeframe of Hypomesus evolution, which was compared with work on similarly distributed taxa. Results Hypothesized trans-Pacific Ocean relationships based on lateral line scale counts were not supported by the phylogeny, suggesting parallel evolution of this phenotype, although we found one such relationship between the western H. japonicus and the two eastern Pacific species (H. pretiosus and H. transpacificus). Dispersalist approaches rejected an early proposal of a double-compression vicariant mechanism as well as an eastern Pacific origin. Results from thelagrangeanalysis suggested a more widespread ancestor, although also supporting a role for the western Pacific. Divergence estimates suggested that most splits between species occurred in the mid-Miocene, and the most recent speciation event, between the eastern Pacific species, occurred in the Pliocene to early Pleistocene. Main conclusions Our molecular data indicate that the character historically used to define relationships within Hypomesus, lateral line scale count, does not reflect ancestry within the genus. Biogeographical reconstructions suggest an important role for the western North Pacific in the diversification of Hypomesus. While uncertainty remains over the date of origin for this genus, estimates place the divergences during periods of climatic cooling that have been important in generating diversity in a number of similarly distributed organisms. Additional comparative data will provide further insight into the relative importance of the western region in generating diversity in the North Pacific Ocean.