The crustose coralline alga Lithophyllum stictiforme is an important reef builder, forming coralligenous concretions in the Mediterranean Sea. This algal species complex is composed of eight cryptic species (or clades). The objective of our study was to compare light-dependent physiological processes within and between the two most abundant cryptic species (C1 and C4) of L. stictiforme from the Bay of Marseille (France). Physiological rates of respiration, photosynthesis and calcification were measured using incubation chambers under various irradiance levels and in the dark during the summer period. We compared the physiology of the C1 and C4 cryptic species of L. stictiforme among three algal groups: C1 (the most common in the Marseille area) from 28 m depth, C4 from the same site and depth, and C1 from a deeper site at 45 m depth. We found both interspecific (between C1 and C4) and intraspecific (within C1) physiological differences. Photosynthetic parameters showed acclimation to light (or depth) with higher values of initial slope of photosynthetic light response curve (α) and lower values of saturating irradiance (Ek) and compensating irradiance (Ec) for C1 from 45 m than for C1 and C4 from 28 m depth. At the shallower depth, significant physiological differences were observed between C1 and C4 with a higher value of maximum rate of gross photosynthesis (Pg max) in C4, suggesting better ability to grow under high irradiance. Light and dark calcification rates differed only between C4 from 28 m and C1 from 45 m depth, being intermediate in C1 from 28 m depth. On a 24 h basis, diel net calcification rates were significantly higher in specimens from the shallower waters than from the deeper waters. Physiological differences suggest physiological plasticity within the regionally dominant cryptic species C1 and species-specific physiological traits between the cryptic species C1 and C4.