The genus Silurus is an important group of catfish species unevenly distributed in Eurasian freshwaters. Including economically important and endangered species, it has attracted the attention of biologists involved in separate subdisciplines. However, the lack of phylogenetic framework leaves unresolved the mechanisms behind the accumulation of a substantial portion of the genus diversity in East Asia. Herein, we combined 89 newly generated and 20 previously published mitogenomes from 13 morphological species to reconstruct phylogenetic relationships, biogeographic history, and estimate species diversity of the genus Silurus. Phylogenetic reconstructions yielded eight clades supported by both Maximum Likelihood and Bayesian Inference. Sequence-based species delimitation analyses yielded multiple Molecular Operational Taxonomic Units in several taxa including Silurus asotus complex (four) and S. microdorsalis (two), suggesting that species diversity is underestimated in the genus Silurus. A reconstructed time-calibrated tree of Silurus species provides an age estimate of the Most Recent Common Ancestor approximately 37.61 million years ago (Ma), and splits among clades within the genus occurred between 11.56 Ma and 29.44 Ma, and among MOTUs within species between 3.71 Ma and 11.56 Ma. Biogeographic reconstructions support China and Korean peninsula as the most likely ancestral area and several dispersal events to Europe and Central and Western Asia are inferred between 21.78 Ma and 26.67 Ma and multiple dispersal events to Japan are inferred between 2.51 Ma and 18.42 Ma. The Eocene–Oligocene extinction event, onset and intensification of the monsoon system, glacial cycles and associated sea-level fluctuations appeared to be important driving forces in the genus.