Abstract To investigate the prebiotic potential of alginate oligosaccharides (AOS), prepared through enzymatic hydrolysis of alginate polymer, the effects of AOS on bacterial growth were studied. In vitro studies showed that the numbers of bifidobacteria or lactobacilli were greater than those in control medium when they were cultured in the medium supplemented with AOS ( P Bifidobacterium bifidum ATCC 29521 and Bifidobacterium longum SMU 27001 more significantly in comparison with fructo-oligosaccharides (FOS). The acidity of the medium with AOS decreased following almost the same trend as that of medium with FOS. In vivo studies showed that AOS selectively stimulated the cecal and fecal microflora of male Wistar rats. The number of fecal bifidobacteria of the rats fed a diet supplemented with 2.5% AOS for 2 weeks increased by 13-fold and 4.7-fold when compared with those fed the control diet and a diet supplemented with 5% FOS, respectively. The number of lactobacilli of the rats fed the diet containing 2.5% AOS increased by 5-fold compared with the controls. In contrast, AOS significantly decreased the abundance of enterobacteriaceae and enterococci ( P