Both defatted peanut flour (DPF) and peanut protein isolate (PPI) are widely used to prepare peanut protein hydrolysates. To compare their enzymatic hydrolysis efficiencies, DPF and PPI were hydrolysed by Alcalase, Neutrase, Papain, Protamex and Flavorzyme. Alcalase and Flavorzyme were found to be the most efficient proteases to hydrolyse both DPF and PPI. The efficiency was comparable to each other when using Alcalase, while PPI was hydrolysed less efficiently than DPF when using Flavorzyme. Analysis of changes in the protein solubility, subunit and conformation, and amino acid composition of DPF, PPI and their Flavorzyme hydrolysis residues indicated that the PPI preparation process had minimal effect on it, but peptide aggregation via non-covalent bonding (including hydrophobic interactions and hydrogen bonds) during hydrolysis and/or thermal treatment after hydrolysis were likely responsible for the reduced hydrolysis efficiency of PPI by Flavorzyme.