The in vitro fermentation of two Non-Digestible Oligosaccharide (NDO) preparations, Arabinoxylan- Oligosaccharides (AXOS) and Oligofructose (OF), and their respective monomeric sugars, xylose and fructose, were investigated by hindgut microbiota of two major aquaculture fish species, Siberian sturgeon (Acipenser baerii) and African catfish (Clarias gariepinus). Inocula from the hindgut of both fish species were incubated for 48 h in bottles containing 1.0% of one of four substrates, i.e. AXOS, OF, xylose or fructose. Amounts and profiles of produced Short-Chain Fatty Acids (SCFAs) differed between the two fish species and substrates. The hindgut microbiota of Siberian sturgeon has a higher fermentation capacity than the microbiota from African catfish. Xylose was much easier fermented than AXOS by microbiota from Siberian sturgeon whereas OF was quicker fermented than fructose with African catfish inoculum. The SCFAs were dominated by acetic acid for both fish species and for all substrates. Fermentation of OF and fructose by hindgut microbiota of Siberian sturgeon also yielded high amounts of butyric and branched-chain fatty acids after 48 h incubation. Results of this study suggest that AXOS, OF, and their monomeric sugars have an impact on microbial fermentation activity of hindgut microbiota from Siberian sturgeon and African catfish in a substrate and species dependent manner.