Agroecology makes its appearance as a science that seeks epistemological bases different from those of conventional science. However, literature has not been reviewed nor have theoretical reflections been written that explicitly establish the alternatives proposed in agroecology. The objective of this essay was to determine the principal epistemological bases of agroecological theory identified as alternatives to conventional science. Within agroecology, emphasis is placed on alternatives to disciplinarity, epistemological monism and the principle of simplicity, although the reflection and construction of alternative bases for these is still diffuse and shallow. Therefore, more theoretical development in this aspect is required.