Samurai High School, サムライハイスクール
Author/Artist : Kawashiba Hiro
Genre: Comedy, Gender Bender, School Life, Sci-fi, Shounen, Supernatural
Summary from mangaupdates.com
In a modern country where the government is controlled by a Martial Shogun and samurai receive much respect, there lives fraternal twins of the Sakakido family. Kou, the brother, is very feminine, excels at cooking, cleaning, arts and crafts. Tsukiko, the sister, is masculine, loves fighting and is a combat genius. The twins learn about the Samurai High School, where men test their strength and women test their femininity, but the only way they can attend is by swapping places. If they are to be found cheating, they will be executed so they have to overcome their gender differences and maintain their secret.
so far 10 chapters are scanlated and currently in 3 volumes... if you like gender bender manga plus some Gintama-like elements you got to read this one