Authorities say most of the dogs were filthy, scared and living in a house in East Northport that was filled with foul air.
The Suffolk County Society for the Prevention of Cruelty to Animals says a woman faces misdemeanor animal cruelty charges.
The organization says fifty-six dogs were removed from the house. Most were shih tzus and poodles.
Puppy mills often exist to produce purebred puppies in large numbers. Many organizations working to combat animal cruelty say they put animals in deplorable conditions.