Two types of hydrocolloids in two distinct zones of red tamarillo (Solanum betaceum Cav.) mesocarp were resistant to digestive enzymes and exhibited different in vitro prebiotic activities. Low molecular weight tamarillo seed mucilage hydrocolloid that was extracted using 1% citric acid or water encouraged the growth of bifidobacteria and lactobacilli more than the high molecular weight tamarillo pulp hydrocolloid that was extracted using 20 mM HEPES buffer or 72% ethanol. The seed mucilage hydrocolloid was also better in reducing the number of pathogenic bacteria than the pulp hydrocolloid. In vitro fermentation of seed mucilage hydrocolloid resulted in higher production of acetate whereas propionate was formed in higher concentration from fermentation of the pulp hydrocolloid. Both hydrocolloids can produce higher amounts of butyrate than inulin and oligofructose during the fermentation. Tamarillo hydrocolloids can act as prebiotics.