The present study explores how in-service secondary education Greek biology teachers understand aspects of the concept of ecosystem under the assumption that the ecosystem is an ill-defined concept. If it is to be considered a holistic entity, the ecosystem acquires its definitional features within the ecological field of systems ecology, which was developed during the 1950s and 1960s but declined after the 1970s under the pressures of internal inconsistencies and persisting unsolved puzzles. Because of these problems, the 'ecosystem' suffers from serious definitional shortcomings. The present study investigates how in-service secondary education Greek biology teachers address the problem of ecosystem 'systemness' and topics that are intrinsically associated with what kind of system the ecosystem is, such as ecosystem balance and self-regulation. Our research compares the background assumptions that lie behind these topics in the field of systems ecology with the analogous assumptions of biology teachers and demonstrates the presence of inconsistencies. Biology teachers do not share with system ecologists the same background assumptions, encounter difficulties in understanding that behind the ecosystem there is something resembling a structure or organisation and hold an individualist/reductionist view of the ecosystem that complies with current (liberal) ideological considerations of wholes.