["Journal of Research in Science Teaching, Volume 63, Issue 4-5, Page 412-432, May 2026. ", "\nABSTRACT\nMechanistic reasoning is a powerful and vital approach for science students to explain scientific phenomena. Current research on students' mechanistic reasoning aims to enhance unpacking, that is, the identification and description of entities at lower scalar levels. However, even the most comprehensive mechanistic explanation must conceal some mechanistic details due to insufficient knowledge or to maintain coherence. These knowledge gaps, known as “explanatory black boxes,” are significant in science education because they highlight areas of incomplete knowledge, facilitating discussions of explanation quality. We explored the impact of familiarizing students with explanatory black boxes by explicitly referring to them during learning. This “black‐box pedagogy” was implemented in a 14‐h online course focusing on cancer‐onset mechanisms. It involved iteratively highlighting black boxes in mechanistic explanations before delving into deeper mechanisms. Our goal was to examine whether and how this pedagogy may scaffold (a) the learning of mechanisms that span multiple scalar levels and (b) students' understanding of epistemic considerations in the context of black boxes and mechanistic explanations. We analyzed learning outcomes of 10th‐grade biology students in two phases. In the first, we used pre‐ and post‐questionnaires, along with in‐course prompts, to examine shifts in students' construction of mechanistic explanations and students' creation of questions regarding mechanistic details. In the second, students created poster projects and reflective worksheets that offered insights into their decision‐making processes regarding which mechanistic details to include or exclude. Findings indicated that black‐box pedagogy effectively supports students' focus on explicated black boxes and their unpacking, as well as their ability to identify implicit black boxes. In addition, this pedagogy facilitates discussions of epistemic issues related to the unpacking and black‐boxing of mechanistic details. While challenges and limitations exist, particularly in addressing lower‐level molecular mechanisms, this study underscores the importance of explicitly discussing, rather than avoiding, black boxes in the science classroom.\n"]