We have studied the structural modifications of lignins from sisal and flax during their soda-anthraquinone (AQ) pulping and subsequent totally chlorine-free (TCF) and elementary chlorine-free (ECF) bleaching. For this purpose, residual lignins were isolated from pulps, analyzed by Py-GC/MS, 2D-NMR, and GPC, and their characteristics were compared to the "milled-wood" lignin of the raw materials. Soda-AQ pulping caused a preferential removal of S-lignin and cleavage of beta-O-4' linkages, but the structure of the residual lignin remained relatively similar to native lignin. TCF bleaching barely affected the lignin structure, and noticeable amounts of beta-O-4' linkages still occur in these pulps. In contrast, ECF bleaching caused strong modifications in the lignin structure with the complete removal of lignin markers in ECF-bleached sisal pulp. However, residual lignin was still present in ECF-bleached flax pulp, with a predominance of G- and H-lignin units and the presence of beta-O-4' linkages.