The literature on assessing the cognitive processes involved in hypertext comprehension during the past 15 years has yielded contradictory results. In this article we explore a possible factor affecting this situation, mainly the fact that previous works did not control for the potential effects on comprehension of reading strategies in hypertext. In Experiment 1, results showed that reading strategies selectively affect the textbase and the situation model level. The number of different nodes read mainly affected the textbase, whereas the reading order influenced the situation model. In Experiment 2, the analysis of reading strategies replicated the effect of knowledge and coherence found in the literature on linear text comprehension (McNamara & Kintsch, 1996), but it was not replicated in hypertext. Low-knowledge participants learned more by following a high coherent reading order, whereas high-knowledge participants learned more by reading the hypertext in a low-coherence order. We discuss the theoretical and methodological consequences of this approach for the study of hypertext comprehension.