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St. Margaret's was founded in 1965, based on the traditions of Catholic Schools. In the beginning, the school was called St. Margaret's Girls College Kowloon, and only accepted female students. In 2001, the school joined the Direct Subsidy Scheme and started to accept boys. In September 2003, St. Margaret's made history as the first school in Hong Kong to adopt a through-train mode from Primary One to Secondary Six on the same school premises. It was also to be a co-educational, English-medium school.