The deadly reptile was up to 8ft long and was discovered wriggling and snapping in a bath when officers swooped on the pad after uncovering a cannabis factory at a nearby property.
It is believed the alligator had been bought from a dealer and taken to the £125,000 three-bedroomed house in Runcorn, Cheshire.
Officers also found a King Cobra, three monocled cobras and a rattlesnake during searches of the reptile dealer’s shop in neighbouring Warrington.
In the first raid, also in Runcorn, police seized a poisonous snake while uncovering a cannabis factory in an upstairs bedroom.
Officers seized around 60 plants and equipment for heating and lighting the plants and a number of tanks housing snakes in the property. A number of dead venomous snakes were also found.
Wildlife officers and specialist reptile handling staff were brought in to deal with the live animals and they are now being cared for elsewhere.
Cheshire Police said a 33-year-old man was arrested in Widnes on suspicion of cultivating cannabis, abstracting electricity and possessing dangerous wild animals. He was released on police bail pending further enquiries.
Insp Dave Gordon said: “This operation was initiated by information we received from members of the community, we were concerned for the safety of the public, so swift and decisive action was taken.
”Some of the animals seized are extremely dangerous, indeed potentially lethal, they have been taken to a safe location where they will remain for the time being in the care of reptile specialists.”