The goals of the present study were to evaluate the suppressive capability of anaerobically digested slurry (ADS) against Phytophthora capsici and to determine the key factors of disease control in ADS. This was achieved by the investigations of the changes in microbial populations and the levels of antimicrobial compound during anaerobic digestion (AD). AD had no significant impact on the numbers of antagonistic fluorescent pseudomonads or Bacillus sp. The contents of total phenolics, volatile fatty acids and sugar fed with the raw slurries to the reactors were decreased by AD. However, the bioreactor effluents had higher concentrations of humic substances and ammonia than the feedstocks. Moreover, AD had a different influence on the content of amino acid in the pig manure compared to the dairy manure. The results obtained indicated that the key inhibitory factors of ADS might be attributed to ammonia and humic substances. (C) 2013 Elsevier Ltd. All rights reserved.