The purpose of this research was to search for a learning hierarchy among skills comprising formal operations and the integrated science processes. Ordering theoretic and probabilistic latent structure methods were used to analyze data on five process skills and six logical thinking skills collected from 700 science students. Both linear and branching hierarchical relationships were identified within and across the two sets of skills. Most of them fit the logical hierarchies which have guided curriculum development and classroom practices in the past. But a few run counter to our present logic and understanding of these skills.