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The actual and negative problem of the ecology of Kola North is the growth of anthrogenous influence on ecosystems of the Arctic seas. We carry out biochemical investigations of sea and freshwater ecosystems of Kola North in the conditions of man-made pollution. These investigations are actual for ecological estimation of state of water ecosystems. The important direction of our research is the development of the complex biochemical system of the biotesting and monitoring of water ecosystems of North Basin. Advantages and limitation of the biochemical monitoring methods are discussed in our works. Our investigations concern such important problem as the ecological biochemistry of fishes of North Basin (the Barents Sea, the Norwegian Sea, the White Sea). The actual task of the contemporary ecological biochemistry is the search and the installation of the effective biochemical molecular markers, determinating the replied reactions of hydrobionts on man-made pollution of the water ecosystems in the conditions of Kola North. The scientists suggest such biochemical indicators as the content of tokoferols, carotines, enzymes, glutation, retinol, aminoacids and others. We suggest such effective and modern molecular bioindicators as the content of carotinoides, macroergic compounds (ATP), the activity of the proteases in the muscle tissues of north fishes, which fix the replied reactions of north hydrobionts on environmental pollution. Effective molecular indicators give possibility to determine the mechanism of biochemical adaptation of fishes.