The Indian Ocean is an area in which a rich suite of cetacean fauna, including at least two subspecies of blue whale, is found; yet little information beyond stranding data and short‐term surveys for this species is available. Pygmy blue whale (Balaenoptera musculus spp.) call data are presented that provide novel information on the seasonal and geographic distribution of these animals. Acoustic data were recorded from January 2002 to December 2003 by hydrophones at three stations of the International Monitoring System, including two near the subequatorial Diego Garcia Atoll and a third southwest of Cape Leeuwin, Australia. Automated spectrogram correlation methods were used to scan for call types attributed to pygmy blue whales. Sri Lanka calls were the most common and were detected year‐round off Diego Garcia. Madagascar calls were only recorded on the northern Diego Garcia hydrophone during May and July, whereas Australia calls were only recorded at Cape Leeuwin, between December and June. Differences in geographic and seasonal patterns of these three distinct call types suggest that they may represent separate acoustic populations of pygmy blue whales and that these “acoustic populations” should be considered when assessing conservation needs of blue whales in the Indian Ocean.