1-Butyl-3-methylimidazolium hexafluorophosphate ([C4MIM][PF6])/DNA and 1-methyl-3-propylimidazolium hexafluorophosphate ([C3MIM][PF6])/DNA mixtures were prepared and characterized by high-pressure infrared spectroscopy. Under ambient pressure, the imidazolium C2–H and C4,5–H absorption bands of [C4MIM][PF6]/DNA mixture were red-shifted in comparison with those of pure [C4MIM][PF6]. This indicates that the C2–H and C4,5–H groups may have certain interactions with DNA that assist in the formation of the ionic liquid/DNA association. With the increase of pressure from ambient to 2.5 GPa, the C2–H and C4,5–H absorption bands of pure [C4MIM][PF6] displayed significant blue shifts. On the other hand, the imidazolium C–H absorption bands of [C4MIM][PF6]/DNA showed smaller frequency shift upon compression. This indicates that the associated [C4MIM][PF6]/DNA conformation may be stable under pressures up to 2.5 GPa. Under ambient pressure, the imidazolium C2–H and C4,5–H absorption bands of [C3MIM][PF6]/DNA mixture displayed negligible shifts in frequency compared with those of pure [C3MIM][PF6]. The pressure-dependent spectra of [C3MIM][PF6]/DNA mixture revealed spectral features similar to those of pure [C3MIM][PF6]. Our results indicate that the associated structures of [C4MIM][PF6]/DNA are more stable than those of [C3MIM][PF6]/DNA under high pressures.