Samurai Deeper takes place in 1604, the beginning of the Edo era (1603 - 1867), where after the Battle of Sekigahara, Tokugawa Ieyasu has taken over as Shogun, and an era of relative peace has begun.

Many main characters in Samurai Deeper Kyo are based on real people:

• Sanada Yukimura
• Tokugawa Ieyasu
• Tokugawa Hidetada (Benitora)
• Date Masamune (Bontenmaru)
• Sarutobi Sasuke (based on a legend, not a real person)
• Kirigakure Saizo

and several lesser characters.