He has conducted field research in a number of African countries (particularly, Tanzania, Nigeria, Benin, Rwanda, Zambia, Uganda) and among Black people in Russia and the United States.

Bondarenko was a visiting scholar with the Northwestern University (United States), Institut für Geschichte (Germany), and Maison des sciences de l'homme (France).

Social theory, anthropological and historical theory, political anthropology, pre-industrial societies, cultures and history of Africa, socio-cultural transformations and intercultural interaction in contemporary world (including ethnic, racial, and religious aspects, migration issues) with special focus on Africa and people of African descent worldwide Bondarenko has introduced (together with Andrey Korotayev) and started elaborating the notion of homoarchy to be coupled with the one of heterarchy, noting that the heterarchy (defined as "the relation of elements to one another when they are unranked or when they possess the potential for being ranked in a number of different ways") is not the opposite of any hierarchy all together, but is rather the opposite of "homoarchy", defined as "the relation of elements to one another when they are rigidly ranked one way only, and thus possess no (or not more than very limited) potential for being unranked or ranked in another or a number of different ways at least without cardinal reshaping of the whole socio-political order".

He has contributed to the studies of the state origins and nature by dealing with such aspects of the problematics as the dynamics of kinship and territoriality as principles of socio-political organization, transformations in ideology, and others.

In publications on contemporary issues Bondarenko argues, in particular, that globalization should be viewed as a primarily cultural, not economic and political, phenomenon which is by no means a recently appeared one but which embraces essentially the whole human history, and which can turn out a "successful historical project" in the shape of a "federation of local civilizations" only.