The potentially lethal American reptile was found wriggling and snapping in a bath when officers went to the address after uncovering a cannabis factory at a nearby property.
It is believed the alligator had been bought from a dealer before being taken to the 125,000 pound three-bed 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, the Daily Mail reported.
In the first raid at another house 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.
Cheshire Police said yesterday that a 33-year-old man was arrested in Widnes on suspicion of cultivating cannabis, abstracting electricity and possessing dangerous wild animals.
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He was released on police bail pending further enquiries.
"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," Inspector Dave Gordon said.
"The animals were seized as part of a joint operation involving local police, Halton Borough Council staff, wildlife officers and reptile experts. Some of the animals seized are extremely dangerous, indeed potentially lethal," he said.
"They have been taken to a safe location where they will remain for the time being in the care of reptile specialists," he added.
A search of a business premises in Widnes revealed some minor breaches of legislation under the Pet Animals Act that were dealt with by Halton Borough Council staff.
But during the search at the house in Runcorn, officers found the alligator, a snake and other reptiles.
The alligator, classified as a dangerous and wild animal, was removed from the property by the council using its powers under the Dangerous Wild Animals Act.