Pygmy blue whales (Balaenoptera musculus brevicauda) are ≤24.1 m and are generally found north of 52°S in summer, whereas the more southerly Antarctic blue whales (B. m. intermedia) may exceed 30 m. Previous assessments have assumed that catches and recent surveys south of 60°S recorded Antarctic blue whales, but these may have included pygmy blue whales. Here, we use ovarian corpora, which accumulate with ovulations and hence with length, to separate these subspecies. The resulting Bayesian mixture model, applied to 1,380 Northern Region (north of 52°S and 35°–180°E) and 3,844 Southern Ocean (south of 52°S) blue whales, estimated that only 0.1% (95% credibility intervals 0.0%–0.4%) of the Antarctic region blue whales were pygmy blue whales and, unexpectedly, found significantly lower lifetime ovulation counts for pygmy blue whales than for Antarctic blue whales (7.6 vs. 13.6). Over four decades, despite substantial depletion of Antarctic blue whales, there was no trend in the estimated proportion of pygmy blue whales in the Antarctic. Several lines of investigation found no evidence for sizeable numbers of pygmy blue whales in ovarian corpora data collected in the 1930s, as was previously hypothesized.