I am new here, but I know that Nystatin works mainly or only in the colon, and that Diflucan works systemically. So if you think candida is infecting various parts of the body, you might want Diflucan. However, it is different for everyone, if one doesn't work, the other might work. I think Dilfucan will kill fungus in your toes and Nystatin will not. This is what I have heard.