The itching could be due to flea allergy dermatitis, but that should go away with the fleas being gone. Have you checked him to make sure there are no fleas remaining?
He could also be itchy from a medical condition or an environmental or food allergy or just dry skin. If he's been to the vet and been given the all clear then it may not be medical.
If it is a food allergy then a diet change would be in order. Many dogs have grain allergies which can be rectified with a switch to grain free food.
If it is dry skin then there are several things you can do. You can give him an oral supplement for his skin and coat like fish oil or extra virgin coconut oil. I use Nupro supplements and extra virgin coconut oil for my pack. You can also bathe him with a moisturizing shampoo and conditioner.
It will be a process of trial and error to figure out what the cause of the problem is though so it will take time.
You know, our Dakota has issues with dandruff as well but his is due to the heat and humidity of being in the south. He never had a problem when we lived in WA state.
I've tried a number of different dog shampoos and I have 3 favorites, they are:
-Bio-Groom Natural Oatmeal Shampoo (I love everything from the Bio-Groom line though)
-Earthbath Tea Tree & Aloe (I also love everything from the Earthbath line)
-Fresh 'n Clean Oatmeal & Baking Soda
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~~Val~~