Fucoidan is a sulfated polysaccharide, purified from brown algae. It has multiple biological activities including anti-cancer and anti-inflammatory effects. Our previous reports demonstrated that fucoidan can stimulate spleen cells and especially high molecular weight fucoidan is responsible for the immunostimulatory activity. However, we recently found that the activity of fucoidan can be dependent on its individual batch or sources. Four different fucoidans (fucoidan A, fucoidan B, high molecular weight fucoidan, and low molecular weight fucoidan) were used for this study. MTT assay and flow cytometry analysis were performed for analysis of the activity of fucoidan. MTT assay showed that fucoidan B significantly decreased the cellular activity of spleen cells compared to fucoidan A. In addition, fucoidan B consistently killed spleen cells based on the cell size by flow cytometry analysis and the morphology by an inverted microscope. To elucidate the detailed mechanisms of cytotoxicity, fucoidan B-treated spleen cells were stained with Rhodamine 123 solution and Annexin V-FITC/propidium iodide for measurement of mitochondrial membrane potential (MMP) and early/late apoptosis, respectively. From these two assays, fucoidan B decreased the MMP and induced early apoptosis of spleen cells. Taken together, we suggest that different batches or origin of fucoidan may have differential activities on spleen cells, immunostimulatory and cytotoxic activity. The present study may provide some valuable information regarding use of fucoidan in the clinical area and in basic research.