Patriarch Kirill held prayers at a research station before taking a walk with the animals.
A picture of the 69-year-old kneeling eye-to-eye with one went viral.
Russia has 10 research stations in the Antarctic, able to accommodate up to 120 people. Patriarch Kirill visited one, the Bellingshausen research station on the island of Waterloo.
The Russian Orthodox church near the Bellingshausen station, which opened in 2004, is the only church on the continent to hold services all year round, with priests spending the winter there.
Church officials said Patriarch Kirill prayed for polar researchers, including 64 Russians who have died on polar expeditions.
The patriarch’s visit was the first ever by the head of the Russian Orthodox Church to Antarctica. It followed the first encounter between a head of Russian Orthodox Church and a pope in nearly 1,000 years.
Since becoming Pope in 2013, Pope Francis has called for better relations between the different branches of Christianity.
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