I understand that it is very popular in Japan. However, it did not originate there.
The first version of this puzzle has been dated back as far as 3000 years ago in Rome. The modern variant was created by an American in 1979, and its popularity surged in Japan under the name 数字は独身に限る, which was later shortened to "sudoku." It started to be published regularly in Britain during the late '90s, and returned to America under its new name.