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 safely with the "extremely dangerous, indeed potentially lethal" 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.
''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, they have been taken to a safe location where they will remain for the time being in the care of reptile specialists.
Police said the raids took place on Friday after they found the snakes whilst uncovering the cannabis factory.
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 a 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 Halton Borough Council using its powers under the Dangerous Wild Animals Act.
At a business premises known as Leroy's Lizard lounge in Warrington, police officers and council staff located a large king cobra, three monocled cobras and a rattle snake.
The dangerous animal offences will be dealt with by Halton Borough Council, prosecuting authority in relation to the Dangerous Wild Animals Act 1976.
These animals were handed over voluntarily by the owners of the business to specialist officers. Alligators which have an average of 75 teeth can grow to 14.5 feet long and weigh over 1,000 pounds.
The largest ever recorded was found in Louisiana and measured 19 feet 2 inches.