Many people swear by yoghurt as a natural remedy - not only eating it but also topically for certain sorts of thrush!
Here are some suggestions from a fairly reliable medical site:
"Home remedies for thrush are aimed at decreasing risk factors for thrush as well as preventing overgrowth of Candida yeast.
Brush the teeth with a soft toothbrush.
Rinse the mouth with a diluted 3% hydrogen peroxide solution.
Rinse the mouth with warm saltwater.
Avoid mouthwash as it can alter the normal flora of the mouth.
Keep dentures clean and see a dentist if they do not fit correctly.
Eat unsweetened yogurt while taking antibiotics.
Lactobacillus acidophilus supplements may help maintain a healthy balance of Candida.
Home remedies that may reduce the discomfort of thrush include
drinking cold liquids, or eating frozen or ice treats;
eating soft, easy-to-swallow foods;
drinking from a straw if the patches are painful.
Gentian violet (1%) is a natural treatment that sometimes works as treatment for thrush. It is a dye that kills bacteria and fungi, and it is available without a prescription. Talk to a doctor before using gentian violet. Grapefruit seed extract is sometimes used by nursing mothers who have developed thrush of the nipples. It can be applied topically (on the skin) or taken orally. Consult a doctor before using this or any supplement."
Something not mentioned there is changing your toothbrush once it has cleared or you will reintroduce the infection. And taking probiotic capsules should help - you get yoghurt with added probiotics but there aren't that many, capsules will provide a much larger number.