Black soybeans (Glycine max (L.) Merr.) have been widely used as a health food and medicinal herb in oriental medicine. In the present study, the chemical structures of two water-soluble polysaccharides (black soybean polysaccharide 1 (BSPS-1) and black soybean polysaccharide 3 (BSPS-3)) isolated from black soybeans were characterized by high performance size-exclusion chromatography (HPSEC), methylation analysis, and 1D ( 1 H, 13 C) and 2D (COSY, TOCSY, HSQC, NOESY, and HMBC) NMR spectra. The molecular weights of BSPS-1 and BSPS-3 were 1.95 × 10 5 and 1.88 × 10 5 Da, respectively. Methylation analysis and NMR spectra indicate that BSPS-1 is composed of 1,6-α-D-glucopyranosyl residues. By contrast, BSPS-3 is mainly composed of a 1,3-β-D-galactopyranosyl residue backbone with side chains substituted at the O-6 position consisting of large content of T-α-L-Araf-(1→ residues, and small contents of →5)-α-L-Araf-(1→, →2)-α-L-Rhap-(1→, and 4-O-Me-β-DGlcAp-(1→ residues. Our results suggest that BSPS-1 is a linear (1→6)-α-D-glucan, whereas BSPS-3 is a type II arabinogalactan. The unique structures of BSPS-1 and BSPS-3 indicate that they might have wide applications in food and pharmaceutical industries.