The ISOMED (A Stable ISOtope database of MEDiterranean marine food web components) database gathers published and unpublished data of δ13C and δ15N values and elemental contents (C and N) of basal sources (i.e., organic matter) and consumers collected in the Mediterranean Sea. Published data refers to scientific peer-reviewed papers selected in the literature through a systematic search. In contrast, unpublished data correspond to the raw δ13C and δ15N data underpinning mean values provided by the authors of the present paper. Data from open-access repositories was not included, as they are already easily accessible. The dataset consists of 4959 georeferenced records spread all around the Mediterranean Sea, spanning 35 years (1983-2018). ISOMED database consists of a unique tool that could help researchers investigate trophic interactions and energy flows in the marine food web of the Mediterranean Sea.