Definition of ISOMER. 1. : one of two or more compounds, radicals, or ions that contain the same number of atoms of the same elements but differ in structural arrangement and properties. 2.: a nuclide isomeric with one or more others.See isomer defined for kids. ADVERTISEMENT.. : one of two or more compounds, radicals, or ions that contain the same number of atoms of the same elements but differ in structural arrangement and properties. 2. : a nuclide isomeric with one or more others. See isomer defined for kids.