Agriculture, both at global and european levels, is in a crisis that originates from a complex set of social, economic and ecologic problems. In this context, agroecology positions itself as a scientific paradigm that can effectively improve agricultural sustainability. To achieve that, researchers need systematic methodologic tools to engage rural populations in the search for solutions. Two complementary methodologies have been developed in the context of Agroecology Research: the firts is MESMIS, within the farmework of Analysis of Agricultural Systems; the second is the Participatory Research Action. While MESMIS provides guidelines at farm level, PAR is a framework to articulate several hierarcical levels, from farm to society, by including the temporal dimension into the analysis. This paper discusses the origin, contributions and limitations of both methodologies.