There are many causes of flaking scalp. It could in fact still be dandruff even though it occurs only in patches. Another cause is infection, either from bacteria or fungi. Bacterial infections are usually caused by staphylococcus species and tend to cause inflammation, redness, and pain. Fungal infections are more common and in fact are one of the most common causes of flaking skin. Tinea capitis (fungal infection of the scalp) is caused by a number of fungal species. Seborrheic dermatitis is another common cause of flaking scalp. While we are not entirely sure what causes it, it is thought to be an abnormally excessive reaction by the immune system to a harmless fungus that is present on everyone's skin.
The first line of treatment for all of these is hygiene. Shampoo every day with a dandruff shampoo and make sure to let it sit for at least 5 minutes before rinsing off. If fungal in origin, a good start is a selenium based shampoo like Selsun Blue or coal-tar based shampoo like Neutrogena T-Gel. These are good for both generic dandruff and toxic to many species of fungi. You may also need more specific anti-fungal topical creams, and in the case of seborrheic dermatitis, some low strength steroid creams are sometimes used to get it under control initially.
Besides dandruff as a simple cause of flaking scalp, there are a wide variety of infectious pathogens responsible for scalp infection that can cause symptoms. A careful examination of the hair disease, microscopic and pathologic evaluation of your hair and skin, and discussion of the cause of your condition with a dermatologist
or your primary care doctor
is the best way to begin a treatment regimen to solve your problem.