Based on both total energy calculations and comparison of experimental and calculated characteristics of the photoelectron spectrum (PHES), the structural assignment of clusters Ag n − (n = 13−16) and Cu m − (m = 14−17) has been made using the density functional theory (DFT) model with our previously developed S2LYP functional. A comparative study of size dependence of geometry, electronic structure, and physicochemical properties has been carried out for a series of anionic silver and copper clusters containing up to 20 atoms. For the cases when two isomers contribute to the experimental PHES, the isomerization barriers and molar ratio of isomers were estimated. It has been shown that the geometry and the properties that are determined mainly by ns-derived electronic states are similar for copper and silver clusters. However, due to the larger contribution of (n−1)d-electrons to the chemical bond, the potential energy surface of copper clusters is less smooth, and these clusters are characterized by higher isomerization energies compared to silver clusters. The isomerization energies of clusters and the number of isomers with similar energies increase with enlarging cluster size. Thus, clusters containing less than 20 atoms easily overcome the barriers of intramolecular isomerization (i.e., behave like liquids). However, it is expected that cooled clusters containing several tens of atoms will have a rigid geometry due to high intramolecular isomerization energies.