Black rot fungus appears when orchids stand in water for too long or their planting medium rots. The symptoms are brown or plum-colored areas on the leaves that turn black. Root rot fungus occurs when the roots have stayed too wet for too long. The symptoms are leaves that turn "leathery" in appearance then yellow. Botrytis cinerea, also known as petal blight, exists when there are high levels of humidity during the dark, cool night hours. Small dark pin dots appear on the flowers to announce the presence of Botrytis.
If your plants are packed tightly together, with little air flow between them, you have invited fungus to develop. A clean growing area with good air flow and appropriate light discourages fungus. Sterilize your pots between uses. Sterilize any tools you use on one plant before using them on another to prevent the spread of problems.
The first step is to quarantine the affected orchids from the rest of your collection. Home orchid growers do not have many choices for fungicides, fewer still for orchid fungicides, and fewer still for orchid fungicides that can be used indoors. Read and follow the instructions on your chosen fungicide. Repeated applications may be necessary.