This study conducts a textbook analysis in the frame of the following working hypothesis: The transformation of scientific knowledge into school knowledge is expected to reproduce the problems encountered with the scientific knowledge itself or generate additional problems, which may both induce misconceptions in textbook users. Specifically, we describe four epistemological problems associated with how the concept of "ecosystem" is elaborated within ecological science and we examine how each problem is reproduced in the biology textbook utilized by Greek students in the 12th grade and the resulting teacher and student misunderstandings that may occur. Our research demonstrates that the authors of the textbook address these problems by appealing simultaneously to holistic and reductionist ideas. This results in a meaningless and confused depiction of "ecosystem" and may provoke many serious misconceptions on the part of textbook users, for example, that an ecosystem is a system that can be applied to every set of interrelated ecological objects irrespective of the organizational level to which these entities belong or how these entities are related to each other. The implications of these phenomena for science education research are discussed from a perspective that stresses the role of background assumptions in the understanding of declarative knowledge.