Different sulfated polysaccharides have distinct abilities to activate specific fibroblast growth factor (FGF) signaling pathways in FGFR1c-expressing BaF3 cells. In the current study, we first isolated and characterized different fucoidan fractions from Sargassum maclurei and Saccharina japonica. All of the fucoidan fractions were incubated with BaF3 cells in the presence of FGF-1, -2, -7, -8, -9, and -10, respectively, to evaluate their FGFs/FGFR1c signal-activating ability. Our data showed that low molecular weight fucoidan fraction from S. japonica with highest sulfate content (LMWF-2M) had the most potent activity among all of the six tested FGFs. Low sulfated heteropolysacchairde fraction LMWF-0.5M, along with SMP-1, SMP-D-1, and SMP-A-1, only activated the FGF-2/FGFR1c pair (P<0.05). In contrast, SMP, SMP-A, and SMP-D stimulated BaF3 cell proliferation except for FGF-8. Both LMWF-1M and LMWF-2M facilitated FGF-1-, -2-, -8-, and -9-based signaling. The sulfate content was the major contributing factor to the observed activity followed by the molecular weight. The monosaccharide composition also affected the activity, in that SMP and its derivatives with varied monosaccharide composition could not induce BaF3 cell proliferation in the presence of FGF-8. The structure-activity relationships revealed in current study provided useful information for the potential application of fucoidans in FGF/FGFR signaling regulation.