This study aimed to quantify resistant starch (RS) contents in native and modified starches from various botanical sources using standard methods for RS analysis (AOAC Methods 991.43, 2002.02, and the Englyst method) to better understand differences in RS contents of starchy foods analyzed using these methods. RS contents of octenyl succinic (OS) normal corn starch increased with increasing wt% substitution, whereas RS contents of OS-modified high-amylose maize starch decreased. Differences in RS contents of RS3 were within 10% regardless of the method used. The largest differences were observed in cross-linked wheat distarch phosphate and debranched high-amylose maize stearic-acid complex (RS5) analyzed using AOAC Method 991.43 and other methods. Differences in RS contents were partially attributed to binding-site differences between Bacillus licheniformis (BL) and porcine pancreas (PPA) á-amylase. Starch granules treated with BL and PPA at equal activity showed distinct morphological changes after 84 h of hydrolysis. Starches hydrolyzed by BL were mainly eroded on the surface of the granules, whereas PPA showed pitting on granule surfaces. Banana starch granules were hydrolyzed mainly in distal regions of the granule. These results suggest that mechanistic differences in enzyme action are responsible for differences in measured RS contents of native and modified starches.