Mesodinium rubrum is a kleptoplastidic ciliate that sequesters the chloroplasts and nuclei of cryptophyte algae to perform photosynthesis. Blooms of M. rubrum can cause red tides in coastal oceans worldwide. Such red tides are detectable by remote sensing, and studying M. rubrum pigments and optical properties is a crucial step toward characterizing its blooms using satellite observation. Previous studies have shown that M. rubrum photoacclimates, modifying its pigment content depending on irradiance. Using cultures at different irradiance levels, we observed that photoacclimation in M. rubrum closely resembles that of its cryptophyte prey Teleaulax amphioxeia, leading to substantial phenotypic variability. In both species, phycoerythrin 545 cellular concentrations increased 3-fold between the highest and lowest irradiance, suggesting a major role in photoacclimation. Absorption cross-section decreased, and pigment-specific absorption coefficients increased with irradiance at the peak absorption wavelengths of chlorophyll a and phycoerythrin 545. After assessing the variability of absorption properties in M. rubrum, we combined field measurements and high-resolution Sentinel-2 satellite images to estimate chlorophyll a concentration of a coastal red tide and document small-scale spatio-temporal features. This work provides an overview of pigment photoacclimation in a peculiar phytoplankter and suggests guidelines for future studies of M. rubrum blooms.