The devotees packed an indoor stadium at the church's global headquarters in Gapyeong, east of the capital Seoul, and listened to Moon's 70-year-old widow Hak Ja Han deliver a eulogy on his life and legacy.
During the ceremony, delegations from South Korea and overseas climbed the stage to lay flowers before a giant backdrop showing a smiling Moon in a black suit and tie.
In the two years since the religious leader died aged 92 of complications from pneumonia, the church he founded appears to have been functioning normally.
Revered by his followers but denounced by critics as a charlatan who brainwashed church members, Moon was a deeply divisive figure.
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His shadowy business dealings saw him jailed in the United States.
The teachings of the Unification Church are based on the Bible but with new interpretations, and Moon saw his role as completing the unfulfilled mission of Jesus to restore humanity to a state of "sinless" purity.
While it claims a worldwide following of three million, experts suggest the core membership is far smaller.