The main purpose of this study was to investigate the distribution and areas of mixing of two stocks of the humpback whale, a krill predator, in the Indo-Pacific region of the Antarctic. These were breeding Stock ‘D’ off Western Australia and breeding Stock ‘E1’ off Eastern Australia. Both stocks have shown sign of recovery after heavy commercial exploitation in the last century. Information on distribution and areas of mixing in the Antarctic feeding grounds is essential to assist the interpretation of abundance estimates. Published mitochondrial DNA (mtDNA) sequences were available for Western Australian (n= 185) and Eastern Australian (n= 104) whales. These were compared with sequences of humpback whales in the Antarctic feeding grounds for Areas IIIE (35°-70°E, n= 95), IVW (70°-100°E, n= 140), IVE (100°-130°E, n=90), VW (130°-160°E, n= 69), VE (160°E-170°W, n=85) and VI (170°-120°W, n=64). In addition, the Antarctic samples were analyzed with a set of eleven microsatellite DNA loci (independent nuclear DNA marker). The genetic analyses were based on biopsy samples. Results of the combined analyses suggested the following: i) Western Australian whales distribute mainly in Areas IV, and probably mix with a different stock in Area IIIE; ii) Western Australian whales do not distribute in Areas V and VI, at least in substantial numbers; iii) Eastern Australian whales distribute mainly in Area VW, and probably mix with a different stock in Area VE; Area VI is occupied by a different stock. This information on distribution and areas of mixing should be used in the interpretation of the abundance estimates of the Western and Eastern Australian stocks in the Antarctic, which has been based on the boundaries of IWC Management Areas. Several additional analyses were suggested to refine the information on pattern of distribution and mixing of humpback whales stocks suggested in this study.