Polysaccharides have been isolated at pH 6.0 or 2.0 from fruits and leaves of two varieties of baobab (Adansonia digitata L.). The isolation protocol was designed to study the influence of pH on the structural and functional characteristics of polysaccharides. The polysaccharides were examined by means of sugar composition analysis, NMR spectroscopy, size exclusion chromatography (SEC) and dilute solution viscometry. Polysaccharide yield was substantially higher in fruits (~20% w/w) than in leaves (~4% w/w) with all samples having low protein content (<~0.5% w/w). Monosaccharide and NMR analysis revealed that polysaccharides extracted from leaves have characteristics of “linear” and “branched” pectins (~71 mol% uronic acids, ~12 mol% rhamnose and ~9 mol% galactose) whereas those from fruits were primarily xylogalacturonans (~69 mol% uronic acids, ~13 mol% xylose). Polysaccharides from leaves had greater molecular weight (>300 × 103 g mol−1) than fruits (<200 × 103 g mol−1) presenting distinct solution behaviour. Polysaccharides from leaves were only dispersed at low concentrations (~1% w/v) whereas those from fruits may be dispersed at >20% w/v, representing a clear divide in their functional properties and potential applications. Overall, baobab fruits and leaves offer a novel source of polysaccharides for the food or pharmaceutical industries.