The Keepers are an insecticide race, believed to have been created by the Protheans to serve as caretakers of the Citadel. They kept the Citadel in top condition for the 48,000 years between the Protheans disappearing and the Asari re-discovering it. The other species of the Galaxy believe they exist for no other reason than to maintain the Citadel and its systems.
After many failed attempts to find out more about the Keepers, the Citadel Council made it illegal to interfere with their work. They were considered completely harmless to other species and their work in maintaining the Citadel's conditions were considered too important to intervene. As the years went by, people stopped caring about the origin of the Keepers and just let them get on with their work.
 Scan the Keepers
There is a minor subplot assignment called "Scan the Keepers" in the Citadel. In this assignment you must find all 21 Keepers in the Citadel and scan them for research. The assignment is given to you in the Citadel Tower Council Chambers. You earn XP and credits for each Keeper scanned, as they are scanned.
It's revealed later in the game that the Keepers were controlled by the Reapers. They were already on the Citadel long before the Protheans arrived. Their main function is to keep the Citadel in top condition so that new species will want to settle there. The Keepers are also created to stop the current species from discovering that the Citadel is actually a hidden Mass Relay that leads to Dark Space where the rest of the Reapers are waiting. When a species reaches a certain level of technological advancement, the Keepers will receive a message from the Reaper Vanguard - a single Reaper that has to stay in the Galaxy and watch over the new species until it's time to restart their cycle of galactic genocide. The Message will tell the Keepers to open the Citadel Relay and allow the Reapers to come through and exterminate all species in the Galaxy.
The Protheans managed to cut the Keepers from all ties to the Reapers, however they couldn't do it quick enough to prevent their own destruction. The Keepers now respond only to the Citadel, which is why the Reapers needed Saren to access the Citadel Relay and why they are planning on replacing the Keepers with the Geth.