The present study reports the investigation of capillary electrophoresis (CE) for the separation of the photosynthetic pigments (chlorophyll derivatives as well as carotenoids) together. Various CE methods, such as micellar electrokinetic chromatography, capillary electrokinetic chromatography, and nonaqueous capillary electrophoresis (NACE) are tested, with coated and uncoated capillary columns to evaluate optimal separation conditions using diode array detection. The effect of different type and composition of organic solvents and surfactants on the separation is discussed. Detection limits are found in the range of 1.14–2.45 ppm. According to the system suitability results, the most effective separation is observed using NACE with Aliquat 336 as cationic surfactant in coated capillary and mixture of MeOH-ACN-THF (5:4:1, v/v/v) as solvent. Quantitative evolution is investigated, and recovery percentage values are found to be 96.7–102%.