Trinity Blood: Rage Against the Moons (2001)

Blurb:
In the distant future, set in a post-apocalyptic world that has been destroyed by Armageddon, the war between humans and vampires rages on, playing out in a power struggle between two factions: the Vatican and the New Human Empire. A secret organization called Rosenkreuz Orden, a group of vampire extremists, manipulates the two factions, pitting them against one another to ensure the war escalates. A Vatican special ops group called AX, led by Cardinal Caterina, must use everything they can—even a vampire who preys on the blood of other vampires—to protect the peace effort.

Source: www.anisearch.com/manga/13760