The rate, speed and latency period of germination were defined for seeds of Trifolium subterraneum variety 45 C. The latency period was 12 hours on distilled water. The hypoxic stress was applied at the beginning (T12) and the end of latency period (T24). It consists on the addition of nitrogen (N2) under 1 bar pressure in hermetically closed boxes during 2 hours. The germination of treated seeds was then assessed on distilled water. The germination test during hypoxic treatment showed that the hypoxic stress delayed germination, slowing down its speed and decreasing the final percentage of germinated seeds. In order to better understand this depressive effect observed following the hypoxic treatments, total endopeptidase activity was measured along with an analysis of protein profiles of seeds with and without hypoxic treatments. While the total endopeptidase activity increased during seed germination, it decreased after hypoxic treatments. The electrophoresis profiles of the different categories of storage proteins, extracted from hypoxic and normoxic seeds, were analysed by 1D SDS-PAGE. The different protein fractions were characterised by the presence/absence, intensity and electric mobility (molecular weights) of the bands. Total seed proteins were then separated by two-dimensional electrophoresis (2D-SDS-PAGE) based on their isoelectric points and their molecular weights. A statistical analysis (ANOVA test) revealed 26 spots for which the volume varied significantly during normoxic seed germination. Furthermore, the volume of 5 spots varied after the hypoxic treatments. In order to establish the first reference proteome map for T. subterraneum seeds during germination and to identify proteins affected by hypoxic treatments, we have subjected all spots to MALDI-TOF-TOF mass spectrometry analysis. Results will be discussed in relation to a potential tolerance and mobilisation of storage proteins during germination under hypoxic treatment.