Sequence stratigraphy is a major research subject in the geosciences academia and the oil industry. However, the geoscience education literature addressing students' understanding of the basic concepts of sequence stratigraphy is relatively thin, and the topic has not been well explored. We conducted an assessment of 27 students' conceptions of four central principles of sequence stratigraphy. Ten juniors, 15 seniors, and two graduate-level students were enrolled in undergraduate stratigraphy courses at three research-intensive universities in the midwestern United States. Fifty percent of students were majoring in geology and forty percent in environmental geosciences. Data collection methods included semistructured (videotaped) interviews, which were conducted after the sequence stratigraphy lectures. Using constant comparative analysis, we documented students' conceptions about eustasy, relative sea level, base level, and accommodation. Results indicated that students poorly integrated temporal and spatial scales in their sequence stratigraphic models, and that some alternative conceptions are more deeply rooted than others, especially those related to eustasy and base level. Additionally, students frequently omitted subsidence as another controlling factor on accommodation. Other findings indicated a low level of familiarity with the classic marginal marine profile and associated sedimentary structures. This study documents the most critical concepts likely to be resistant to conceptual change through instruction in sequence stratigraphy.