The present paper focuses on ninth graders difficulties in learning ecology. Three dimensions in addition to the macrolevel dimension were identified as basic obstacles that might hinder students meaningful learning of ecology the microlevel dimension relating to the molecular and micro processes of matter and energy transfer in ecosystems the spatial dimension of ecosystems regarding simultaneous occurrences in space and the multiple roles of their biotic elements and the time dimension relating to long-term evolutionary forces acting in ecosystems. These four dimensions were examined in students understanding of the concept of food chains in ecosystems. Four ninth grade classrooms participated in the study. Two of the classes studied ecology in the traditional mode and served as a control. Two classes were exposed to a novel specifically designed learning context for ecology study which integrated several elements known to influence learning including a special curriculum to guide students active involvement in a self-regulated process of inquiry. A qualitative analysis of students written responses and recorded verbal interactions was used as well as simple quantitative methods. copy 2002 Wiley Periodicals Inc. Sci Ed86 645 ndash 671 2002 Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/sce.10041