Dinoflagellates of the genus Dinophysis are the most persistent producers of lipophilic shellfish toxins in Western Europe. Their mixotrophic nutrition requires a food chain of cryptophytes and plastid‐bearing ciliates for sustained growth and photosynthesis. In this study, cultures of D. acuminata and D. acuta, their ciliate prey Mesodinium rubrum and the cryptophyte, Teleaulax amphioxeia, were subject to three experimental settings to study their physiological response to different combinations of light intensity and quality. Growth rates, pigment analyses (HPLC), photosynthetic parameters (PAM‐fluorometry), and cellular toxin content (LC‐MS) were determined. Specific differences in photosynthetic parameters were observed in Dinophysis exposed to different photon fluxes (10–650 μmol photons · m−2 · s−1), light quality (white, blue and green), and shifts in light regime. Dinophysis acuta was more susceptible to photodamage under high light intensities (370–650 μmol photons · m−2 · s−1) than D. acuminata but survived better with low light (10 μmol photons · m−2 · s−1) and to a prolonged period (28 d) of darkness. Mesodinium rubrum and T. amphioxeia showed their maximal growth rate and yield under white and high light whereas Dinophysis seemed better adapted to grow under green and blue light. Toxin analyses in Dinophysis showed maximal toxin per cell under high light after prey depletion at the late exponential‐plateau phase. Changes observed in photosynthetic light curves of D. acuminata cultures after shifting light conditions from low intensity‐blue light to high intensity‐white light seemed compatible with photoacclimation in this species. Results obtained here are discussed in relation to different spatiotemporal distributions observed in field populations of D. acuminata and D. acuta in northwestern Iberia.