Like most countries do have their own national flower, Japan has two "national" flowers which are chrysanthemum and cherry blossom although they are not prescribed by law as national flowers. I would like to focus on chrysanthemum in this article.
This flower is used as the Imperial seal of Japan which is called the Chrysanthemum Seal. In Japan each family has its own family crest which is inherited from generation to generation. Suppose you make Kimono (Japanese traditional clothing) which you wear at the time of formal ceremony such as a graduation, wedding and funeral ceremony etc etc., you usually put your family's crest mark on Kimono to show which family you are from. Also tombstone of each family does have its own crest. In the case of Imperial family members, chrysanthemum flower seal has been used as a crest.
Therefore the crest of chrysanthemum is used for the badges worn by Japanese congress members, a front page of Japanese passport, decorations or medals awarded by the Japanese Government etc etc. Until the end of the world war II, all the warships of Japanese Imperial Navy did have chrysanthemum emblem placed on the front of warships.
In relation to this particular flower, here is a very interesting and famous book by the title of "The Chrysanthemum and the Sword: Patterns of Japanese Culture". Following is the outline about this book from Wikipedia.
QUOTE
The Chrysanthemum and the Sword: Patterns of Japanese Culture is an influential 1946 study of Japan by American anthropologist Ruth Benedict. It was written at the invitation of the U.S. Office of War Information, in order to understand and predict the behavior of the Japanese in World War II by reference to a series of contradictions in traditional culture. The book was influential in shaping American ideas about Japanese culture during the occupation of Japan, and popularized the distinction between guilt cultures and shame cultures.
UNQUOTE
In a sense the flower of Chrysanthemum can be said to be not only the Japanese Imperial family's crest but also the symbol of the country of Japan.
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