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Environmentally-friendly implementation of new technologies and eco-innovative solutions often faces additional secondary ecological problems. On the other hand, existing biological systems show a lesser environmental impact as compared to the human-made products or technologies. The paper defines a research agenda for identification of underlying eco-inventive principles used in the natural systems created through evolution. Finally, the paper proposes a comprehensive method for capturing eco-innovation principles in biological systems in addition and complementary to the existing biomimetic methods and TRIZ methodology and illustrates it with an example.