JKA stands for the Japan Karate Association (or Nihon Karate Kyokai in Japanese). The JKA is the original and oldest Shotokan Karate organisation. It was established in 1949 by the founder of the Shotokan style, Gichin Funakoshi.
Today the JKA is the largest and most prestigious Shotokan Karate organization in the world.(http://www.jka.or.jp/) It is present in more than 100 countries. Karate propagated out of Japan mainly because of the efforts of the JKA, which began sending its highly accomplished professional instructors throughout the world as early as 1958. In October 1957 the 1st JKA All Japan Karate Championship was held in Tokyo. This was the 1st tournament in the history of Karate. Yet the JKA was established by Sensei Funakoshi (its Chief Instructor), as an organization whose purpose was, and is, to train True Karate Masters _ to teach Karate as a way of life, and not merely to organize tournaments. JKA Karate is Bushido: it is based on the way and forged by the spirit of the ancient Japanese warrior. Since 1957, JKA tournament rules are the simplest of all: no gloves, masks, protective clothing and weight categories are imposed. Just win or lose with the first deadly blow (without actually hitting your opponent). JKA is 'The Keeper of Karate's Highest Tradition'.
Other Shotokan organizations not associated with the JKA, are either direct off-shoots of the JKA, (headed by ex-members of the JKA), or are indirect groups only very remotely connected to the JKA. Often these indirect groups will claim some form of lineage to the JKA or Funakoshi Sensei, usually through a complex family-tree of federations.
It must be stressed that the only organization ever supported officially, publicly and physically by Sensei Funakoshi until the week before his death was the JKA.