Reef-building corals (Order: Scleractinia) are undergoing rapid taxonomic revision after molecular systematics challenged traditional relationships at all taxonomic levels within the group. New morphological characters based on fine-scale morphological features are being used to produce evolutionary relationships that support molecular phylogenies. While these fine-scale morphological characters (micromorphological characters and microstructural characters) are starting to be used to revise taxonomy, their variation and stability have not been fully explored. In order to determine their stability for use in taxonomy, I performed a series of aquaria-based experiments to test the stability and explore the variation of fine-scale morphology in response to differing environmental conditions. Temperature, light intensity, and environmental pH were chosen as the varied environmental factors in three sets of experiments. These factors were chosen to test stability of fine-scale morphology because of their importance in calcification rate, their importance to reef health, and their potential for environmentally-driven plasticity. In order to better examine the range of variation present in these cases, each variable was assessed at three different environmental levels. The total range of variation was assessed using scanning electron microscopy (SEM) to examine differences in the skeletons were constructed and also to examine transverse sections of the corallites using thin-sections. Macro-scale variation was assessed using geometric morphometrics. While variation within fine-scale morphology was found in response to each environmental factor being altered, the variation did not alter the interpretation of the fine-scale morphological characters. The skeletal variations observed were minor and did not alter the interpretation of character states. I found that micromorphological and microstructural characters were stable for use in taxonomic revision with the caveat that ranges of variation do occur and should be taken into consideration.