Late-embryogenesis-abundant (LEA) proteins accumulate as plant seeds desiccate and also in vegetative organs during periods of stress. They are predicted to play a role in plant stress tolerance. In the present study, we have initiated the characterization of phosphorylated LEA proteins present in the Arabidopsis seed, using a strategy that combines the thermostability (solubility upon heating) of many LEA-type proteins with the use of phosphoaffinity chromatography to obtain an enriched subpopulation of phosphoproteins. The specificity and efficiency of the procedure was assessed by alkaline phosphatase treatment and by a specific stain for phosphoproteins, in addition to the immunodetection of AtRab18, a phosphorylated LEA protein present in the mature dry seed. The phosphoproteins were identified by MS either by PMF using MALDI-TOF MS after 2-DE separation, or by peptide sequencing using both capillary LC MS/MS (LC muESI-ITMS/MS) and nanoLC coupled to nanoESI-MS/MS (LC-nanoESI-Q-TOF-MS/MS). Several LEA-type and storage-like proteins were identified as components of the phosphoproteome of the Arabidopsis seed.