Red coral (Corallium rubrum) is an important component of the Mediterranean coralligenous habitat. The present study analyzes the relationship between energy storage molecule concentration (i.e. tissue balance of protein–carbohydrate–lipid levels) and the gonadal output in two populations located at different depths (16–18 m and 40–45 m depth) through a seasonal cycle (2002–2003). In June 2003, another six populations have been sampled to compare medium-scale geographical variation. The colonies sampled were less than 6 cm high, thus representing the majority of the population in the studied area. There was no clear relationship between energy storage (i.e. carbohydrate and lipid levels) and gonadal output, nor in the seasonal cycle or the spatial variation. A clear-cut seasonal trend of energy storage was detected only in the shallower population. The water temperature was warmer at 20 m depth and the water transparency (Secchi disk) was also higher (lower seston concentration) in 2003 when the same periods in 2002 and 2003 were compared (May–August). Carbohydrates seemed to be more sensitive to food constraints than lipids. The partial mortality detected in summer 2003 in the sampling area appeared to be recorded in the carbohydrate and lipid levels of this species, especially in the shallow population. The biochemical levels prove to be a useful tool to detect unusual environmental conditions that may cause partial or total mortality in benthic suspension feeders.