The characterization of the molecular composition of organic carbon in both gaseous and aerosol is key to understanding the processes involved in the formation and aging of secondary organic aerosol. Therefore a technique using active sampling on cartridges and filters and derivatization followed by analysis using a thermal desorption–gas chromatography–mass spectrometer (TD–GC–MS) has been used. It is aimed at studying the molecular composition of organic carbon in both gaseous and aerosol phases (PM2.5) during an intensive field campaign which took place in Corsica (France) during the summer of 2013: the ChArMEx (Chemistry and Aerosol Mediterranean Experiment) SOP1b (Special Observation Period 1B) campaign. These measurements led to the identification of 51 oxygenated (carbonyl and or hydroxyl) compounds in the gaseous phase with concentrations between 21 and 3900 ng m−3 and of 85 compounds in the particulate phase with concentrations between 0.3 and 277 ng m−3. Comparisons of these measurements with collocated data using other techniques have been conducted, showing fair agreement in general for most species except for glyoxal in the gas phase and malonic, tartaric, malic and succinic acids in the particle phase, with disagreements that can reach up to a factor of 8 and 20 on average, respectively, for the latter two acids. Comparison between the sum of all compounds identified by TD–GC–MS in the particle phase and the total organic matter (OM) mass reveals that on average 18 % of the total OM mass can be explained by the compounds measured by TD–GC–MS. This number increases to 24 % of the total water-soluble OM (WSOM) measured by coupling the Particle Into Liquid Sampler (PILS)-TOC (total organic carbon) if we consider only the sum of the soluble compounds measured by TD–GC–MS. This highlights the important fraction of the OM mass identified by these measurements but also the relative important fraction of OM mass remaining unidentified during the campaign and therefore the complexity of characterizing exhaustively the organic aerosol (OA) molecular chemical composition. The fraction of OM measured by TD–GC–MS is largely dominated by di-carboxylic acids, which represent 49 % of the PM2.5 content detected and quantified by this technique. Other contributions to PM2.5 composition measured by TD–GC–MS are then represented by tri-carboxylic acids (15 %), alcohols (13 %), aldehydes (10 %), di-hydroxy-carboxylic acids (5 %), monocarboxylic acids and ketones (3 % each), and hydroxyl-carboxylic acids (2 %). These results highlight the importance of polyfunctionalized carboxylic acids for OM, while the chemical processes responsible for their formation in both phases remain uncertain. While not measured by the TD–GC–MS technique, humic-like substances (HULISs) represent the most abundant identified species in the aerosol, contributing for 59 % of the total OM mass on average during the campaign. A total of 14 compounds were detected and quantified in both phases, allowing the calculation of experimental partitioning coefficients for these species. The comparison of these experimental partitioning coefficients with theoretical ones, estimated by three different models, reveals large discrepancies varying from 2 to 7 orders of magnitude. These results suggest that the supposed instantaneous equilibrium being established between gaseous and particulate phases assuming a homogeneous non-viscous particle phase is questionable.