We investigated demographic history and population structuring of Colossoma macropomum sampled from 14 localities in the Amazon basin and the Bolivian sub-basin; the two basins are separated by a series of 16 rapids. Although genetically differentiated, IMa analyses suggest non-zero bi-directional migration rates, and inter-basin divergence of approximately 17 thousand years ago. Analyses in BEAST indicated that Bolivian C. macropomum has been demographically stable except for a moderate population increase in the last 12 thousand years, while Amazonian C. macropomum has been experiencing demographic growth over the last 350 thousand years, resulting in approximately one order of magnitude increase in coalescent Ne. © 2010 Elsevier Inc.