In this study, we explored undergraduate chemistry education at Kotebe University of Education (KUE) in terms of the ontological orientations, patterns and source domains of educators' and undergraduate students' sense of the atom. Due to the ambiguity and controversy regarding atomic ontology as a case of interest and the requirement for a thorough analysis, an interpretative case study design was employed. It mainly involved a semi-structured interview of 10 educators and 14 undergraduate students. The analysis involved Charmaz's approach for coding. Four core patterns were found to constitute the overall narrative of educators and undergraduate students, from which the interpretative, mechanical, and hypothetical orientations were implied. The ways of thinking in the three patterns were traced back to the underemphasis and distorted portrayal of the History and Philosophy of Science (HPS) in the curriculum and classroom discourse. The usage of some words and expressions with mechanical connotations was also discovered to be the fourth theme of patterns to which the mechanical orientations are attributed. Views of controversial ontologies are held by the participants of this single system. There is also an emerging inclination among undergraduate students toward reductionism, which is not expected from a chemistry student. Therefore, this study implies that the historical and philosophical aspects need to be critically examined in classroom instruction, curriculum development, professional development of educators, and research on chemistry education to avoid ontological complications and address learning impediments. The instructional approaches, materials, and classroom discourse also need to be examined carefully from an ontological point of view to avoid unnecessary complications and obstacles.