Thermal fingerprints for seeds of 20 crop wild relatives of Brassicaceae stored for 8 to 44 years at the Plant Germplasm Bank-Universidad Politécnica de Madrid and Royal Botanic Gardens Kew Millennium Seed Bank were generated using differential scanning calorimetry (DSC) and analysed in relation to storage stability. Poor-storing oily seeds tended to have lipids with crystallization and melting transitions spread over a wide temperature range (c. 40°C) that spanned over the storage temperature, plus a melting end temperature around 15oC. We postulated that in dry storage the variable longevity in Brassicaceae seeds could be associated with the presence of meta-stable lipid phase at the temperature at which they were being stored. Consistent with that, when high-quality seed samples were assessed after banking at −5 to −10°C for c. 40 years, melting end temperatures were much lower (c. 0 to −30°C) and multiple lipid phases did not occur at the storage temperature. We conclude that multiple features of the seed lipid thermal fingerprint could be used as biophysical markers to predict potential poor performance of oily seeds during long-term storage.