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, is the son of Monju, the chief priest of the Taihaku Shrine. In this shrine, Monju's former teacher, Mahoroba, is imprisoned. Problems arise when Mahoroba escapes, gains power, and transforms Monju into stone.

The story features Yakumo's first steps with a Shikigami, training with Izuna (the Taihaku Shrine's resident miko,) and seeking Mahoroba through various Japanese historical dates. Famous Japanese historical characters such as Oda Nobunaga can be seen throughout the manga.

Source: Wikipedia, Edited.