The present study investigated the association of students' fundamental ideas and misconceptions about ontological features of atom identity and behavior with the formation of their portrayed representations of the atomic structure. Participants (n = 421) were secondary education students in the eighth, tenth, and twelfth grades. Students' portrayed representations of the atomic structure were accessed through drawing tasks, while their understanding of the ontological features of atom was measured through a specially designed questionnaire. Latent Class Analysis (LCA), a psychometric method, was applied to the elementary features of the portrayed representations to classify them and test the potential coherence of their representations regarding atomic structure. The LCA revealed three latent classes, which showed a relative coherence in three of the anticipated models, "Particle model," "Nuclear model," and "Bohr's model." Moreover, students' conceptions and misconception about the ontological features of atom were used as covariates in the LCA and their effects on the above-mentioned class-memberships were estimated. Results indicated a significant effect of students' conceptions of the atomic ontological features on their portrayed representations of the atomic structure. Implications for theory and practice are discussed.