This study provides a baseline describing natural small scale variability of Symbiodinium density in the sentinel coral Acropora globiceps during the summer, under non-bleaching conditions. Spatial scales investigated range from the colony scale (1–10 cm, i.e. among branches of the same colony) to the reef scale (1–10 km, i.e. among stations distributed over several locations and depths), at Moorea Island, French Polynesia. The coral–Symbiodinium symbiosis is a key process in scleractinian coral physiology, and Symbiodinium density provides an easy-to-measure and inexpensive biomarker of this symbiosis health. Spatial variability of three major environmental factors: light intensity, sedimentation and water motion was also assessed to evaluate their potential link with Symbiodinium density. Density of Symbiodinium did not significantly differ within colonies or among colonies within a station. However, a marked depth gradient was observed, showing increasing density with increasing depth and decreasing light intensity. These observations provide an interesting reference for forthcoming comparisons with disturbed conditions, such as bleaching events.