This paper presents a generally applicable method for characterizing subjects' hypothesis-testing behaviour based on a synthesis that extends on previous work. Beginning with a transcript of subjects' speech and videotape of their actions, a Reasoning Map is created that depicts the flow of their hypotheses, tests, predictions, results, and conclusions. The methods are described and then applied to a group of three undergraduate biology students testing hypothesis in an inquiry-based laboratory exercise, the Red and White Yeast Lab. Analysis of hypothesis-testing behaviour via Reasoning Maps reveals most of the features explored in previous studies in a unified context. In addition, Reasoning Maps allow analysis of higher-order patterns in hypothesis testing that are not possible using existing methods. We have designed these methods so that they will provide a common language for analysing and understanding hypothesis testing that will allow global comparisons of behaviour.