This article explores the alignment of learning outcomes to assessments in science classrooms; and also what high school teachers do to incorporate higher order thinking skills in teaching science. I argue that science teachers do not always align learning outcomes to what they assess in science classrooms. My argument is that if HODs and science teachers do not incorporate HOT skills in science teaching, South Africa isfar away from improving Physical Science matric results. Data was collected through document analysis and semi structured interviews with 12 Science heads of departments (HODs) and senior teachers, who are experienced in teaching high school Physical Sciences. They are the curriculum leaders and experts in schools. The mixed methods (quantitative and qualitative) approach was used. This study adopts interpretive research paradigm. Data analysis revealed that while HODs and science teachers understand what HOT and CT skills are, they do not incorporate them in science teaching. Another finding is that learning outcomes were not aligned to assessments, which caused problems when learners write National Senior Examinations (NSE). This paper suggests that HOD s incorporate and model HOT skills to science teachers and science teachers need to further model HOT skills to grade 12 science learners. This might help in improving Physical Sciences National NSE results. This paper further suggests models that can be used to effectively teach HOT skills across disciplines.

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