This study investigated the effect of annealing treatment (at 50°C for 72 h) on hydrolysis of tapioca and sweet potato starches using a raw starch hydrolyzing enzyme namely STARGEN 001 (a blend from fungal α-amylase and glucoamylase) at sub-gelatinization temperature (35°C) for 24 h. The degree of hydrolysis of the starches was evaluated based on the dextrose equivalent (DE) value. The hydrolyzed starches were then characterized in terms of its morphology, swelling power and solubility, gelatinization and pasting properties, amylose content and x-ray diffraction pattern. After 24 h of hydrolysis, annealed starches were hydrolyzed to a greater degree with higher DE value compared to native starches (40% vs 33% for tapioca; and 29% vs 24% for sweet potato starch). Scanning electron microscopy (SEM) micrographs revealed a more porous granules and rougher surface in annealed starches than their native counterparts. The swelling power and solubility of annealed starches decreased significantly. Annealing was found to affect the pasting properties of the starches appreciably and increase the starch gelatinization temperature. The amylose content in hydrolyzed annealed tapioca and sweet potato starches increased while no significant changes observed in the X-ray diffraction of those starches. This study shows that the annealing treatment can be used as a way to increase the degree of hydrolysis of tapioca and sweet potato starches at sub-gelatinization temperature using a raw starch hydrolyzing enzyme.