For a long time now, the Capital Kingdom of Regunum has kept its dominance over the land during the raging wars, and kept the world at peace. There are, however, the recent appearances of humans who held within them great mystical power, the "inousha" (literally translated as "a person with a gift/talent"). The people started fearing these inoushas, and began to detest them. Because of this, the capital of Regunum carry out a movement to seize and capture all inoushas within the land to keep the people at bay.
At this time, Ruca, the son of a merchant living in Renugum, discovers that he also holds the same mystical power...
(Source: OneManga)

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)