The Sisters of Silence were the militant arm of the Adeptus Astra Telepathica during the Great Crusader.
Their current standing in the 41st Millenium however is unknown. There are no canonical references to their fate. Some fans believe that they now help man the Black Ships. Some believe they were either completely annihilated at the height of the Horus Heresy, protecting the Emperor's "secret project". Others, including myself, believe that they have been incorporated into the Inquisition.
The Adeptus Astartes is comprised of autonomous Chapters, each of which is a complete army in itself, possessing its own transport, warp-capable spacecraft, non-combatant personnel and fortress-monastery based on a planet or fleet. There are roughly a thousand Chapters, each led by a Space Marine with the rank of Chapter Master. A chapter's fighting force numbers a nominal 1,000 Marines, divided into ten companies, each of which is commanded by a Captain. Companies are further divided into squads of ten battle-brothers.
The Chapter Masters owe their allegiance to the Emperor. Ultimately the Chapter is subject to the orders of the highest-ranking among the Adeptus Terra, although only in a general sense.
Chapters are monastic communities in nature; for most of the Marines, the Chapter is their world, and the only contact they have with outsiders is in battle.