I don't think you can "treat" this at home. Never had a case of it so I'm just specualting on what little I do know.

Figure out a way to get to a vet for antibiotics and cleaning of the reptile’s mouth with antiseptic. Depending on how bad the case surgery could be needed to remove tissue. Dont put it off, the longer it takes fix the more the infection will spread. I'm not trying to scare you but left untreated for a certain amount of time could lead to death weather it be starvation, pneumonia, etc. Double check your husbandry for possible causes so other dont follow the same path.

Most often times, mouth rot is not the only thing going on - typically there is a systemic infection (something affecting more than one organ / area). Chances are an antibiotic is going to be needed. I would think it would hold true with geckos as it does for snakes to increase the temps a couple degrees to help the body fight the infection. I'd also house the gecko on paper towels. Perhaps cleaning the area with a diluted betadine solution will help, but as far as treatment... I think you will have to look into somehow getting antibiotics. What temp. are you housing the gecko(s) at?

In the case of this gecko in particular, when I got him (keep in mind he was a rescue) I  put him in a very clean new enclosure on paper towels. Normally I house my geckos at 92 degrees on the warm side and around 75 degrees on the cool side. In this instance I had heard that raising the temperature could help so I bumped the temperature up in his enclosure to about 95 degrees. So far I am seeing improvement, he is still very alert and appears to be active and if anything he is a bit underweight.  I have read that the betadine solution helps.. so I'm going to try that.. He seems to be getting progressively better at this point, but If necessary I have a couple of exotic vets in the area, I can go to.  

Iodine or Provodone Iodine solution applied with a clean q-tip daily will help immensely

Hey I just met you. And this is crazy. But award some points. Close this question, maybe?

BAHAHAHAHAHAHA!

+ to you sir!

This question has had no activity for 14 days and will be closed by an administrator unless the original poster takes action.

Recommended Action: Points awarded

An administrator will select responses and assign points at their discretion.

Original poster, please close this question out and assign points. If you have any further information in the resolution of your problem, please post it here so that others may learn from it.