This paper incorporates the interdisciplinary New Institutional and Transaction Costs Economics and suggests a holistic framework for analysis of management agro-ecosystem services. That new approach for analyses and assessment of management of agro-ecosystem services includes: definition of the agro-ecosystem services and the governance; specification of governance needs of agro-ecosystem services and the spectrum of available governing modes (formal and informal institutions, market, private, public and hybrid forms); assessment of efficiency of different modes of governance in terms of their potential to protect diverse eco-rights and investments, assure a socially desirable level of agro-ecosystem services, minimize overall costs, coordinate and stimulate eco-activities, meet individual and social preferences and reconcile conflicts of related agents etc.