Numerous reports have accumulated concerning the quality of solid compost. In contrast, there are few for the residue of anaerobic digestion. In this study, the fertilizer value of anaerobic digestion liquor (ADL) was evaluated, and the effect of aeration on the reduction of the phytotoxicity was examined by a germination assay. Low or high aeration (100 or 400 mL/min) was added to 3 L of ADL obtained from a mixture of pig manure and garbage by using 5-L jar fermenters under a controlled temperature of 30°C. During the 14-day aeration period, a high aeration rate improved the germination index (GI) score from 5.7% to nearly 80%, while a low aeration rate did not. Although organic matter decomposition, determined as chemical oxygen demand, did not differ with aeration intensity, remarkable differences were observed in the time course of changes in pH, electric conductivity and ammonium-nitrogen (NH4-N) and total nitrogen (T-N) content. Among these parameters, the NH4-N concentration correlated highly with the GI score (r = 0.986). The primary phytotoxic element in ADL was considered to be NH4-N, and the stripping of ammonia (NH3) by high aeration resulted in the improvement of the GI score. Although the ratio of major nutrients N : P2O5 : K2O (1:0.41:0.94) in ADL was at nearly same level as conventional liquid fertilizer, special attention should be paid to the high concentration of NH3 when drawing up a fertilization plan.