The research focus on children's science has recently shifted from separate concepts to more comprehensive and complex topics. This study addressed pupils' understanding of the complex topic of energy flow and matter cycling. A scoring system with three categories and six concepts was developed and used by four biology teachers to analyze 106 pupils' concept maps. The results indicate that most of the pupils failed to recognize the interrelationships among the various concepts concerned with units of energy flow and matter cycling. It was the relationship between the living world and the non-living world that presented the greatest difficult to understanding. This paper concludes with suggestions for curriculum development and biology teaching. (Contains 5 figures and 4 tables.)