This study assessed the removal efficiency of organic matter and how it relates to the decrease of toxic and mutagenic effects when an anaerobic reactor is used to treat the bleaching effluent from two kraft pulp mills. Parameters such as COD (chemical oxygen demand), DOC (dissolved organic carbon), AOX (adsorbable organic halogen), ASL (acid soluble lignin), color, chlorides, total phenols and absorbance values in the UV-VIS spectral region were measured. The acute and chronic toxicity and genetic toxicity assessments were performed with Daphnia similis, Ceriodaphnia sp. and Allium cepa L, respectively. The removal efficiency of organic matter measured as COD, ranged from 45% to 55%, while AOX removal ranged from 40% to 45%. The acute toxic and chronic effects, as well as the cytotoxic, genotoxic and mutagenic effects, decrease as the biodegradable fraction of the organics is removed. These results, together with the organic load measurement of the effluents of the anaerobic treatment, indicate that these effluents are recalcitrant but not toxic. As expected, color increased when the anaerobic treatment was applied. However, the colored compounds are of microbial origin and do not cause an increase in genotoxic effects. To discharge the wastewater, it is necessary to apply a physico-chemical or aerobic biological post-treatment to the effluents of the anaerobic reactor.