Technical Abstract: The accident at the Chernobyl Nuclear Power Plant (CNPP) on April 26, 1986 is the most serious nuclear disaster in human history. However, while the area proximal to the CNPP remains substantially contaminated with long-lived radioisotopes including 90Sr and 137Cs, the local ecosystem has been able to adapt. We recently proposed a working model for plant adaptation to ionizing radiation based on the results of proteomic analysis of mature soybean seeds harvested from control and radio-contaminated growth-plots in the Chernobyl region (Danchenko et al., 2009). Herein, we extend the initial soybean-based model using the results from a parallel study of flax (Linum usitatissimum). Seeds of the local flax variety Kyivskyi were sown in radio-contaminated and control fields in the Chernobyl region. Total protein fractions were extracted from mature seeds, and analyzed using two-dimensional electrophoresis combined with tandem-mass spectrometry. Expression profiles for 720 protein spots were determined for seeds harvested from both radio-contaminated and control fields. Thirty five of the protein spots differed in expression levels at a p-value of = 0.05. Of these, 28 were identified using state-of-the-art MSE methods. The differentially-abundant proteins were assigned to one of nine functional categories; the two categories containing the most proteins are those associated with signaling and transcription. We propose that seeds produced by plants grown in the radio-contaminated soil conditions of the CNPP area are adapted to a high-IR environment through changes in the levels of proteins associated with multiple signaling pathways, along with an overall decrease in protein flux through secretory pathway.