Wood chips of Eucalyptus globulus and E. nitens were biodegraded by the white-rot fungus Ceriporiopsis subvermispora for periods from 15 to 60 days. Two analytical techniques, oxidation with copper(II) oxide (CuO) and thioacidolysis were used for in situ characterization of lignin, and determination of changes in the amount of syringyl (S) and guaiacyl (G) units, frequency of beta-O-4 linkages and S/G ratio. Wood weight losses after degradation varied from 1 to 10 %. A preferential degradation pattern of lignin over cellulose was observed with lignin losses ranging from 5 to 26 % for both Eucalyptus species. Thioacidolysis analysis showed a reduction in the amount of S units of 42 % and 24 % for E. globulus and E. nitens lignin, respectively. No variation in the amount of G units in the residual lignin of decayed wood chips was observed. The S/G ratio for E. globulus and E. nitens determined by oxidation with CuO was 3.9 and 3.1, respectively. Results showed that during the degradation of Eucalyptus spp. wood by C. subvermispora there were a preferential degradation of syringyl structures and non-condensed aryl-ether bonds of lignin.