The ability of specific strains of probiotic bacteria to remove the pure cyanobacterial peptide toxins microcystin-LR, -RR, -LF, and a combination of microcystins from the cyanobacterial extracts Microcystis PCC 7820 and NIES 107, as well as the cyanobacterial cytotoxin cylindrospermopsin, from aqueous solutions was assessed. The probiotic bacterial strains studied were Lactobacillus rhamnosus strains GG and LC-705, Bifidobacterium lactis strains 420 and Bb12 and Bifidobacterium longum 46, all previously shown to be effective in toxin removal. The maximum removal of microcystin-LR, 60.3%, was observed with L. rhamnosus GG, of microcystin-RR, 62.8%, and microcystin-LF, 77.4%, with L. rhamnosus LC-705, and of cylindrospermopsin, 31.6%, with B. longum 46 (toxin concentration 100 μg L-1, 37 °C, 24 h). Several microcystins could be removed simultaneously as observed by removal of microcystins present in the cyanobacterial extracts. A combination of three probiotic strains enhanced their removal ability as compared to the removal properties of the individual strains. We conclude that specific strains of probiotic bacteria are effective in elimination of different cyanotoxins from solution.