College level students are expected to be able to make sense of, and explain, aspects of chemical bonding and structure in terms of molecular orbital concepts. The present paper derives from in-depth research into the thinking of a small sample of college chemistry students. This study in one UK college revealed the ways in which students found the orbital concept problematic. A previous paper (i?Conceptualizing quanta: illuminating the ground state of student understanding of atomic orbitalsi?) reports how these students struggled to make sense of atomic structure in orbital terms. The present paper considers the studentsi? understanding of the molecular orbital concept. It is suggested that when learners are introduced to ideas about molecular orbitals before they have mastered ideas about atomic systems, then their learning difficulties may be e?compoundedi? in the more complex context. For example, it was found that students often identified the orbitals involved in two-centre bonds as atomic orbitals. Representations of delocalised bonds invoked various alternative interpretations: but were seldom conceptualised as implying poly-centred molecular orbitals. These findings suggest that students are not given sufficient time to construct acceptable models of atoms and molecules as e?quanticlesi?. [Chem. Educ. Res. Pract. Eur.: 2002, 3, 159-173]