This study aims to identify students’ misconceptions regarding covalent bonds. Seventy‐seven graduate students in the middle of Indonesia participated in the study. Data were collected in three stages. First, misconceptions were identified by using the Semi Open Diagnostic Test. Ten students who experienced the worst misconceptions were interviewed. Lastly, textbooks were reviewed. Content analysis was used to analyze the misconception data. We identified eight primary misconceptions, namely: (i) a covalent bond is formed between two atoms with a pair of free electrons; (ii) each atom in a stable molecule must follow the octet rules; (iii) a covalent bond is polar if the electron affinity of two bonded atoms is different; (iv) the form of the molecule depends on the number of atoms bonded to the central atom; (v) nonpolar molecules have a dipole moment µ > 0; (vi) all bonds in polar molecules are polar, while all bonds in non‐polar molecules are non‐polar; (vii) the number of bonds depends on the electronegativity of the atoms; and (viii) bond length depends on the type of bond. The main causes of student misconceptions are as follows: (i) incomplete information; (ii) difficulty understanding basic concepts regarding covalent bonds; and (iii) lack of effective communication between students and teachers. The results suggested the following implications for teaching: the teacher should identify misconceptions about prior knowledge or concepts prior to teaching the basics, identify reference book learning, and facilitate effective communication so that information received by the student is complete and correct. © 2016 Wiley Periodicals, Inc. J Res Sci Teach 54: 520–537, 2017