Brown algae are recognized as bioindicators of heavy metal contamination in coastal waters. Comparison of morphological and functional characteristics of algae living in different environmental conditions is essential for understanding mechanisms of marine organism adaptation to anthropogenic environmental impact. The aim of this study is to determinate concentration of fucoxanthin and heavy metals in branches of brown seaweeds Cystoseira barbata (Stackhouse) C. Agardh and Cystoseira crinita Duby in water areas with different anthropogenic pressures. The content of fucoxanthin in the samples is determined by means of thin layer chromatography, and heavy metals are quantified using atomic absorption spectrophotometry. The maximum concentrations of fucoxanthin (3 mg·g-1 of dry weight), lead (48.5 μg·g-1), zinc (62.6 μg·g-1), and cadmium (3.2 μg·g-1) are found in branches of 2- to 3-month-old seaweeds. The content of fucoxanthin in the branches of C. barbata is 1.5 times higher than that in C. crinita. The Cystoseira seaweeds living in a eutrophic bay have higher concentrations of the pigment and zinc than the macrophytes from open waters. The elevated levels of fucoxanthin in brown algae of this genus found in eutrophic and heavy-metal-polluted water areas demonstrate the important role of this carotenoid in the adaptation of the algal photosynthetic apparatus to anthropogenic environmental changes.