Globally, the Indian Ocean appears to have the greatest blue whale (Balaenoptera musculus ssp) acoustic diversity, with at least four acoustic populations from three defined sub-species. To understand how these different populations use this region as habitat, we first need to characterize their spatial and seasonal distributions. Here, we build on previous passive acoustic monitoring studies and analyze a passive acoustic dataset spanning large temporal (9 years) and spatial (3–9 sites covering more than 12 million km2 of potential acoustic habitat in the southwest Indian Ocean) scales. A novel detection algorithm was employed to investigate the long-term presence of Antarctic blue whale and SEIO and SWIO pygmy blue whale calls. We found that Antarctic and pygmy blue whales have completely different spatial and seasonal distribution in the southern Indian Ocean. Antarctic blue whales are heard almost year-round on the whole array, with great inter-annual variability. The two pygmy blue whales share a highly stable seasonal acoustic presence, but their geographical distributions overlap at only a few central Indian Ocean sites. However, Antarctic and pygmy blue whale acoustic co-occurrence is common, especially in sub-tropical waters. These temporal and spatial distributions strengthen our understanding of seasonal occurrence and habitat use of distinct populations of blue whales in the southern Indian Ocean. A better comprehension of the ecology of Indian Ocean blue whales will require interdisciplinary studies to examine the drivers of the variability seen from passive acoustic studies.