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"There has been constant conflict between the Adeptus Ministorum and the Chapters of the Adeptus Astartes since Fatidicus first began preaching on Terra. They are rivals in power like any Imperial Organisations, but more importantly, their beliefs differ at a very fundamental level. In particular, there is a schism in the clergies thinking concerning the Space Marines. On the one hand the Space Marines, above all others, can truly be called the children of the Emperor. They are wholly his creation and even contain elements of his own genetic structure. They are the founders of the Imperium, and supreme defenders of humanity. The Space Marines are unswervingly loyal to the Emperor and would die in the defence of his honour and the Imperium. However, the Space Marine Chapters do not adhere to the teachings of the Ecclesiarchy. Their beliefs vary wildly from chapter to chapter, worshipping the Emperor and their Primarchs to different degrees. In many ways they are heretics with their own traditions, ceremonies and beliefs, some of which are very barbaric, compared to the well-ordered masses of the Ecclesiarchy.

Most Space Marines worship the Emperor as a great, gifted man, but do not consider him a god in the same sense that is preached by the Ecclesiarchy. His blood runs through their veins and he is considered the ultimate example of mankind, but he is a man nonetheless. Also it is a matter of debate whether the Space Marines are truly human at all. Their genetically engineered bodies are far superior to a normal human, enough to make them a separate race if one wished to interpret their differences so. How can any self-respecting Confessor or Cardinal relate to a monstrous giant who can spit acid, crush a mans skull with one hand and practises crude acts of blood sacrifice.

An uneasy compromise has been reached over the Millennia, which can be summed up as an agreement to differ. The Ecclesiarchy does not send Confessors and Missionaries to the Space marine worlds and the chapters of the Adeptus Astartes do not interfere with the Adeptus Ministorum. Space Marine Chaplains are given their precious Rosarius by the Ecclesiarchy as a symbolic link between the two organisations, but the Chaplains still preach their own version of the Imperial Creed to their brethren. This uneasy truce has been shattered at times when a particularly zealous Cardinal or Confessor has roused the ire of the Space Marine Chapters with his words or deeds. These feuds are usually resolved quickly, though not always without bloodshed, and the relative peace between the two organisations returns."

- from the 2E Codex SoB

Sums it up.