In contemporary global markets evaluation and selection of green strategic partnership has never been so important. The firms are competing not only at the industry level but at the supply chain levels as well, thus raising the importance of green supply chain phenomenon. The firms implementing the eco-innovation strategy realize the need for strategic partnership and collaboration with other supply chain actors. Therefore, the main purpose of this chapter is to develop an approach to evaluate different strategic co-operation partners for different eco-innovation strategies in international value chains. In this study a case of Lithuania is investigated from the co-operation perspective in the development of eco-innovation. Expert assessment and multi-criteria assessment method FARE (factor relationship) is used for the assessment of the types of co-operation means. The findings are important for enterprises, policy-makers and academia involved in eco-innovation development, as they contribute to the existing knowledge by expanding understanding of the co-operation phenomenon and advancing eco-innovation practices.