Most studies on the effects of galactic cosmic rays (GCR) have relied on terrestrial irradiation using spatially homogeneous dose distributions of mono-energetic beams comprised of one ion species. Here, we exposed mice to novel beams that more closely mimic GCR, namely, comprising poly-energetic ions of multiple species. Six-month-old male and female C57BL/6J mice were exposed to 0 Gy, 0.5 Gy, or 1.5 Gy simplified simulated 5 ion GCR (GCRsim). Exposure to microgravity was simulated using hindlimb unloading (HLU). At nine months post exposure, the mice were terminated to assess for the presence of exposure-induced epigenetic alterations. DNA hypermethylation in the 5'-untranslated regions of Lx_III, MdFanc_I, and MdMus_II families of the Long Interspersed Nucleotide Element 1 (LINE-1) was observed in the lungs of male mice. These effects were accompanied by increases in the expression of DNA methyltransferases Dnmt1 and Dnmt3a, and methyl-binding protein, MecP2. Trends towards DNA hypomethylation, although insignificant, were observed in the lungs of female mice in the HLU + 1.5 Gy GCRsim group. Altogether, our findings suggest persistent and sex-specific epigenetic reprogramming in the mouse lung and suggests that the DNA methylation status of LINE-1 can serve as a robust and reliable biomarker of previous radiation exposure.