| Summary: | (1) Background: Trichomycterinae represent 60% of the species in the family and, while seven genera comprise 1–3 species each, <i>Trichomycterus</i> and <i>Cambeva</i> have over 180 known species between them. Although integrative studies aimed to clarify the relationships within the subfamily, the diversity of species of <i>Trichomycterus</i> remains an open question. Herein, we explored an unprecedented sample to investigate the divergence in the lineages of <i>Trichomycterus</i>. (2) Methods: we recovered the phylogenetic relationships of the subfamily using 566 sequences (999 bp) of the mitochondrial gene cytochrome b, calculated intra- and intergroup distance percentages, and estimated divergence times. (3) Results: we recovered 13 highly supported and geographically structured lineages; intergenus divergence was 11–20%, while interspecies divergence was 3–11%; <i>Trichomycterus</i>, <i>Cambeva</i>, <i>Scleronema</i>, <i>Hatcheria</i>, <i>Eremophilus</i>, and <i>Ituglanis</i> were recovered as monophyletic, with three other highly divergent clades: Guiana Shield, Magdalena basin, and Tapajós basin. (4) Conclusions: We propose that the trans-Andean austral clades be allocated into <i>Hatcheria,</i> and the Guiana clade supports a new genus. We also observed that the headwaters nearest the Magdalena and Orinoco basins showed a high diversity and endemism of Trichomycterinae lineages. We discussed the role of geomorphological events and the climatic features which may explain cladogenesis events in Trichomycterinae.
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