The Onmyou Taisenki manga does not tell the same history as the anime. The story happens years before the events in the anime. The main character, Yakumo (who also appears on the anime) is the son of Monju, the chief priest of the Taihaku Shrine. In this shrine, Monju's former teacher, Mahoroba, is imprisoned. The problems start when Mahoroba escapes, gains power, and transforms Monju into stone.
The story of the manga is about Yakumo's first steps with a Shikigami, training with Izuna (Taihaku Shrine's miko) and seeking Mahoroba through various Japanese historical dates. Famous Japanese historical characters such as Oda Nobunaga can be seen throughout the manga. (from the Onmyou Taisenki entry on Wikipedia with slight modifications)
