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Aim We sought to reconstruct the spatio-temporal genetic diversification in goldfish of the Carassius auratus complex, which is widely distributed in Eurasia, to test whether vicariance events or human-mediated translocations best explained lineage divergence and genogeographical history. Location East Asia and the Oriental islands including Japan, the Ryukyus and Taiwan, and Europe, including Russia and the Czech Republic. Methods We reconstructed the matrilineal history of Eurasian goldfish using 1876 sequences from the partial mitochondrial DNA control region (426 bp) and 191 complete sequences of cytochrome b (1140 bp) from 67 localities representing most of the range of the species. Divergence times were estimated using a Bayesian Markov chain Monte Carlo approach based either on molecular clock data or on the fossil record. Genetic structure and the historical demography of populations were analysed using partial correlation tests and analyses of molecular variance. Results Three lineages had high levels of regional specificity. Lineages A and B from the main islands of Japan differed greatly from lineage C, which occurred on the mainland, Taiwan and the Ryukyus. Lineages A and B had late Pliocene origins. Six geographically constrained sublineages within lineage C had near-simultaneous mid-Pleistocene divergences. Main conclusions Genetic structure in the C. auratus complex appears to have been driven by palaeoenvironmental perturbations rather than human translocations. The disappearance of a land bridge in the Tsushima Strait around 3.0 Ma is responsible for the separation of Japanese and continental lineages; the estimated divergence time is 2.75-2.32 Ma. Fujian, China and Vietnam appear to have provided important refugia for the C. auratus complex during glaciation. After warm, moist summer monsoons intensified during the mid-Pleistocene, goldfish are likely to have dispersed north-eastwards to recolonize the Ryukyus via Taiwan and northwards to recolonize mainland China. [ABSTRACT FROM AUTHOR]