- There are three stocks of yellowtail flounder in U.S. waters, the Gulf of Maine/Cape Cod, Georges Bank, and Southern New England/Mid-Atlantic stocks.
- NOAA Fisheries and the New England Fishery Management Council manage Gulf of Maine and Southern New England/Mid-Atlantic yellowtail flounder; NOAA Fisheries and the New England Fishery Management Council collaborate with Canada to jointly manage Georges Bank yellowtail flounder, because the stock spans the international boundary.
- Yellowtail flounder, along with other groundfish in New England waters, are managed under the Northeast Multispecies Fishery Management Plan, which includes:
- Permitting requirements for commercial vessels.
- Separate management measures for recreational vessels.
- Time/Area Closures to protect spawning fish and habitat.
- Minimum fish sizes to prevent harvest of juvenile fish.
- Annual catch limits, based on best available science.
- An optional sector (catch share) program can be used for yellowtail flounder and other groundfish species. The sector program allows fishermen to form harvesting cooperatives and work together to decide when, where, and how they harvest fish.