Eucalyptus nitens wood samples were subjected to consecutive stages of hydrothermal processing for hemicellulose solubilization and delignification with an ionic liquid, i.e., either 1-butyl-3-methylimidazolium hydrogen sulfate or triethylammonium hydrogen sulfate. Delignification experiments were carried out a 170 °C for 10–50 min. The solid phases from treatments, i.e., cellulose-enriched solids, were recovered by centrifugation, and lignin was separated from the ionic liquid by water precipitation. The best delignification conditions were identified on the basis of the results determined for delignification percentage, lignin recovery yield, and cellulose recovery in solid phase. The lignins obtained under selected conditions were characterized in deep by 31P-NMR, 13C-NMR, HSQC, and gel permeation chromatography. The major structural features of the lignins were discussed in comparison with the results determined for a model Ionosolv lignin.