The Sisters of Silence manned the Black Ships during the Great Crusade while a part of an organization known as The Adeptus Astra Telepathica.
Via our good friends at Lexicanum
The Adeptus Astra Telepathica is divided into a recruitment body (the League of Blackships) and a training body (the Scholastia Psykana). These two are united under the Master of the Adeptus Astra Telepathica and his advisory council of several hundred senior officials from the two divisions. They are responsible for the specially trained Astrotelepaths who use their mysterious powers to communicate with others of their kind across vast interstellar distances which separates the worlds of the Imperium. The Astra Telepathica is also known to operate a special decryption and internal affairs branch known as the Cryptaesthesians. During the Great Crusade the Astra Telepathica also operated a unit of Blank psyker-hunters who manned the Black Ships known as the Departmento Investigates, otherwise known as the Sisters of Silence. The numbers of the Silent a Sisterhood dwindled as a result of the Horus Heresy but active units have been observed at the end of the 41st Millennium.
Their ranks consist of psychic servants of the Imperium and these psykers have undergone the Soul Binding ritual with the Emperor. This process passes on some of the Emperor’s strength of will into his servants, thus protecting them from evil, psychically attuned enemies. The ritual ultimately results in blindness though there are a rare few Astropaths who are judged strong enough to warrant them not taking part in the Soul Binding. These individuals are considered the lucky ones, as they do not have to partake in the agonising process as most Astropaths.
It is through the righteous persecution of the Inquisition, combined with the careful testing of the Coven Masters of the Adeptus Astra Telepathica which purges any deviant mutations that are commonly associated with those beings that develop psychic potential. Under Imperial edict, they are allowed their own operatives but they were prohibited from serving as wardens aboard their own vessels. This is because it was far too easy for a malignant psyker to coerce the mind of another telepath. Thus, they used the Sisters of Battle or Inquisitorial Storm Troopers to serve as custodians aboard the Black Ships where their faith protected them from the predations of the mind-witches they guarded.
Before the end of the Horus Heresy, this division within the Imperium held the City of Sight as its headquarters where psykers were taken to its mindhalls for testing. Inside these iron clad halls, the psykers took their first steps in the soul binding ritual and further recruitment into the astropathic choirs.
Due to their duties, the Adeptus Astra Telepathica works in conjunction with the Adeptus Astronomica. Much of the strange properties of the warp remained a mystery to the research theologians of this organization.