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Research into learners' ideas about science suggests that school and college students often hold alternative conceptions about lsquo;the atom’. This paper discusses why learners acquire ideas about atoms which are incompatible with the modern scientific understanding. It is suggested that learners' alternative ideas derive – at least in part – from the way ideas about atoms are presented in the school and college curriculum. In particular, it is argued that the atomic concept met in science education is an incoherent hybrid of historical models, and that this explains why learners commonly attribute to atoms properties (such as being the constituent particles of all substances, or of being indivisible and conserved in reactions) that more correctly belong to other entities (such as molecules or sub-atomic particles). Bachelard suggested that archaic scientific ideas act as ’epistemological obstacles’, and here it is argued that anachronistic notions of the atom survive in the chemistry curriculum. These conceptual fossils encourage learners to develop an ‘atomic ontology’ (granting atoms ‘ontological priority’ in the molecular model of matter); to make the ‘assumption of initial atomicity’ when considering chemical reactions; and to develop an explanatory framework to rationalise chemical reactions which is based on the desirability of full electron shells. These ideas then act as impediments to the development of a modern chemical perspective on the structure of matter, and an appreciation of the nature of chemical changes at the molecular level.