Kwan (Hanja: 館; Hangul: 관) in Korean literally means building or hall, but when used in martial arts it can also refer to a school or clan of martial artists who follow the same style and/or leader.
In the context of taekwondo, the phrase the five kwans refers the first five martial arts schools to open in Korea following the end of Japanese occupation at the end of World War II.
The phrase the nine kwans refers to the original five schools plus four major schools that opened after the conclusion of the Korean War. After the Korean War, students from the original five kwans began opening their own schools (these schools were called "annex kwans"). By 1960, the number of kwans in Korea had increased to 40. Shortly after the Korean War, at the urging of the South Korean government, the Korea Taekwondo Association (KTA) was established to consolidate and unify the kwans. By 1974, the KTA had succeeded in consolidating the 40 schools into just nine major schools. By 1978 the KTA had coordinated the Unification Proclamation, in which all 9 remaining kwans agree to abide by Kukkiwon-style taekwondo and rank promotions. Note however that many of the schools split during this period, with some factions still practicing (even today) their original martial arts styles.