Understanding the degree of genetic exchange between subspecies and populations is vital for the appropriate management of endangered species. Blue whales (Balaenoptera musculus) have two recognized Southern Hemisphere subspecies that show differences in geographic distribution, morphology, vocalizations and genetics. During the austral summer feeding season the pygmy blue whale (B. m. brevicauda) is found in temperate waters and the Antarctic blue whale (B. m. intermedia) in polar waters. Here we used genetic analyses to report on several cases of hybridization between the two recognized blue whale Southern Hemisphere subspecies in a previously unconfirmed feeding season sympatric area off Antarctica. The pygmy blue whales utilizing waters off Antarctica may migrate then breed during the austral winter with the Antarctic subspecies. Alternatively, the subspecies may interbreed off Antarctica outside the expected austral winter breeding season. The genetically estimated recent migration rate from the pygmy to Antarctic subspecies was greater than evolutionary migration rate estimates and previous estimates based on morphology of whaling catches. This discrepancy may be due to differences in the methods or an increase in the proportion of pygmy blue whales off Antarctica within the last four decades. Potential causes for the latter are whaling, anthropogenic climate change or a combination of these, and may have led to hybridization between the subspecies. Our findings challenge the current knowledge about the breeding behaviour of the world’s largest animal and provide key information that can be incorporated into management and conservation practices for this endangered species.