I have had various fly infestations over the years myself. They are attracted to decaying organic material. I have found that I can get rid of them by doing two things:
- Keep your enclosures immaculately clean. The flies are attracted to animal droppings, dead insects, uneaten food, dirty water, etc. In a naturalistic vivarium, this can be difficult. Cleaner organisms, such as isopods, may help.
- Hang flypaper above areas where flies congregate. The fumes are non-toxic, and eventually, every fly will land on it.