The effects of linoleic acid (LA (C18:2)) and its degradation by-products on hydrogen (H<SUB>2</SUB>) production were examined at 37 <SUP>o</SUP>C and an initial pH value of 5.0 using granular and flocculated mixed anaerobic cultures from the same source. In the flocculated cultures, the H<SUB>2</SUB> consumers were inhibited to a greater extent when compared to the granular cultures. The maximum H<SUB>2</SUB> yields were 2.52 +/- 0.2 and 1.9 +/- 0.2 mol mol<SUP>-1</SUP> glucose in the flocculated and granular cultures, respectively. The major long chain fatty acids (LCFAs) detected at which H<SUB>2</SUB> attained a maximum value were LA (750 mg L<SUP>-1</SUP>) and myristic acid (MA) (500 mg L<SUP>-1</SUP>). Bacteroides sp. dominated the granular cultures whereas Clostridium sp. and Bacillus spp. were the major microorganisms in the flocculated cultures. A flux balance analysis (FBA) revealed that homoacetogens consumed more H<SUB>2</SUB> in the granular when compared to the flocculated culture. A principal component analyses (PCA) showed the first three principal components accounted for approximately 76% and 68.5% of the total variability for the LA and its degradation by-products and the T-RFLP data sets, respectively.