The current study aims to investigate students' representations of the atomic structure in a number of student cohorts with specific characteristics concerning age, grade, class curriculum and some individual differences, such as formal reasoning and field dependence/independence. Two specific task contexts, which were designed in accordance with corresponding teaching contexts for the atomic structure, one based on Bohr's model and the other on the quantum mechanical model, were examined as for their potential to differentiate initial students' representations of the atomic structure (when no specific context was provided). Participants (n = 421) were students of 8th, 10th and 12th grades of secondary schools from Northern Greece. Results showed that, although developmental factors, like formal reasoning, were associated with a better representation of the atomic structure, the task context appeared to have the dominant role, since positive associations were found between student cohort characteristics and representation of the atomic structure in context dependent tasks, even after accounting for the effects of individual differences.