Depending on what state you purchase your puppy in and where your puppy was born will determine how many of governing bodies and regulations are involved.

United States Department of Agriculture

The United States Department of Agriculture (USDA) is a federal branch of the U.S. Goverment that oversees everything related to Agriculture. The division called APHIS ( Animal Plant Health Inspection Services ) is responsible for the oversight of Dog Breeders, Distributers, and Transportion of Pet Store Puppies.

Private Inspections & Regulators

The American Kennel Club tracks purebred pedigrees through their Registration. The American Kennel Club inspects AKC Breeders and AKC Pet Stores that sell AKC Puppies.
The American Pet Registry tracks documentation of pedigrees and the registration of purebred dogs and puppies.
American Canine Association is America's largest veterinary health tracking registry. ACA has the Star Breeder program where breeders must complete certain requirements to gain a high star status.

Local Board of Health Departments

The board of health in many states oversees and for some states enforces regulations for pet stores. It also handles customer complaints and can check in on the store to ensure all documentation and sanitary needs are met for the puppies in their care. The board of health for many states inspects and enforces certain codes for pet stores. The board of health will generally do a yearly inspection.

State Departments of Agriculture

Each state has their own department of Agriculture with their own specific regulations regarding the breeding, handling, and raising of puppies.