Analytical alkaline Cu oxide oxidation and ¹³C-labeled tetramethylammonium hydroxide (¹³C-TMAH) thermochemolysis are complementary molecular techniques that provide information about lignin phenols in natural samples. ¹³C-TMAH has the added capability of determining free phenol content of the released methylated monomers, thus allowing assessment of demethylation as well as input from hydrolyzable tannins and other polyphenolics. Capabilities of the two methods were illustrated by analysis of a humic fraction extracted from a rice soil that supported a field study of crop residue management in the Philippines. On-line ¹³C-labeled TMAH analysis detected about 26% greater phenols (syringyl, vanillyl, and cinnamyl) in the humic fraction of a treatment with anaerobic decomposition of crop residues than in the humic fraction of a treatment with aerobic decomposition. This relative phenol accumulation is consistent with observations from longer-term field studies and potentially explains an inhibition of N mineralization that occurred in the anaerobic decomposition treatment. Analysis of the same humic samples by CuO oxidation found that phenol levels differed by less than 2% between the residue treatments. The divergence between the two analytical methods stems from the inability of CuO to measure ortho phenols, which increased mildly in abundance in the anaerobic treatment and represented 50% of the total yield from ¹³C-TMAH in the form of methylated caffeic acid.