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Mallards in Florida during the spring and summer originated from captive-reared stock. We consider these "domestic" mallards a serious threat to Florida's wild waterfowl. Diseases such as duck plague and fowl cholera have been linked specifically to domestic or captive-raised waterfowl, and are easily transmissible to wild ducks.  The potential for such an outbreak is a biological concern. Another significant threat of mallards is the genetic introgression of mallards into Florida's mottled duck population.

Dealing with nuisance mallards is more complicated than controlling muscovies. If mallards are obvious hybrids with muscovies or other domestic ducks (see photo below), then no federal or state wildlife laws protect them from capture or direct population control. These hybrids may be moved to a captive situation where they would not come into contact with wild birds, or humanely euthanized as a last resort. If the mallards have plumage similar to true, wild-strain mallards, and the birds are not marked as captive reared (generally, either marked with a clipped hind toe or a seamless metal leg band), then the birds are protected under federal migratory bird regulations. Destroying eggs or directly controlling populations requires a free mallard control permit.