Using a phenomenographic design, this research reports on a study of a cohort (N = 22) of graduate students' conceptualizations of difference as they progressed through the only required diversity course in a science education program at a large, urban university in the American northeast. Data collection included biweekly course reflections, a modified Pedagogy of Science Teaching Test designed with students labeled with disabilities within its contextual framing, and biweekly 'science for all' lessons created by the participants that were not explicitly framed to address disability. Mixed-methods data analyses addressed to what extent these graduate students developed a critical lens toward difference (i.e., expressed, imagined, and/or imposed variations in human behavior and potential) and explored to what extent these theoretical elements transferred into pragmatic applications by the participants, for example in their lesson planning, that addressed multiple interpretations of difference to provide evidence of their capabilities to bridge theory to practice. Additionally, the case of disability as a marker of difference was also paid special attention to in light of lacking analyses in multicultural science education around issues of disability exclusion and teacher biases toward this marker of difference. The data suggest that while students in this 'urban and multicultural science education' course appear to be able to theorize critically about multicultural issues in urban science education (as per the goal of the course), their capacities to reflect on their pedagogical decisions within contexts that contain students labeled with disabilities, and plan comprehensive 'science for all' classroom learning environments, remained disciplinary focused, no matter if the students labeled with disabilities were the focal marker of difference within these contexts' demographics or not. Emergent data analysis also suggests that disability was the least recognized and interpreted marker of difference, which led to limited ways that students took up this concept in comparison with other forms of difference such as race, class, and gender. Moreover, rather than emphasizing critical pedagogies that are pertinent for transformative change in science education for "all" diverse populations, the participants remained focused on narrowly defined, content-specific ways of teaching and learning science. Implications for this research include focusing on the goals of courses such as this one, attending to the unique case of disability as a liminal realm of conceptualizing difference, and supporting graduate students' needs to aid in bridging the divide between theory and practice for both more traditional markers of difference taken up by multicultural science education (e.g., race, class, and gender) as well as disability as a marker of difference that is under theorized and lacking pragmatic application within such diversity requirement courses.