Swine wastewater is characterized by high organic matter content, solids, nitrogen (expressed as total ammonia and protein) and heavy metals. This work determines the methanogenic toxicity effect of free ammonia contained in swine wastewater comparing raw swine wastewater (RW) and the liquid fraction of swine wastewater (TW). The values of IC50 (50% of inhibition) obtained for methanogenic bacteria ranged between 56 and 84% for RW, meanwhile IC50 for TW was ranged between 84 and 94%. Such inhibitory effects can be related to the free ammonia nitrogen concentration (> 40 mg NH3-N/L) contained in swine wastewater.