Well, Bonsai most likely did not originate in Japan!  No!  Today it is generally accepted that Bonsai as we now know it, most likely began in China in the Sui or Tang dynasties around  589 AD – 907 AD.
However there is more to the story. Old records show that Bonsai definitely moved to Japan from China as a result of trade between the two nations. Exactly when Bonsai became an ‘art’ form and looked like the “Little Trees” we know today is very difficult to estimate. The Japanese are credited with developing the systems for shaping the plants with wire and bamboo only sometime in the late 1700’s to early 1800’s. Before this, container-grown plants in China and Japan were most likely only pruned to control size and growth, important when transporting the plants to trading places. Strong acceptance and appreciation of the concept now known as Bonsai, along with the horticultural skills required to develop and maintain them, soon elevated them to the art form status they enjoy today.

Footnote … sort of?
China and Japan were not the only civilisations to grow plants in containers! This practice is thought to go back at least to ancient Egypt  …  and how about the Hanging Gardens of Babylon?
Egyptians of that era did cultivate perennial plants in containers for decorative use in palaces and temples but not cultivated in the way of modern Bonsai.