With the increasing interest in using bacterial biofilms in geo-engineering practices, such as soil improvement, sealing leakage in earth structures, and hydraulic barrier installation, understanding of the contribution of bacterial biofilm formation to mechanical and hydraulic behavior of soils is important. While mechanical properties of soft gel-like biofilms need to be identified for appropriate modeling and prediction of behaviors of biofilm-associated soils, elastic properties of biofilms remain poorly understood. Therefore, this study investigated the microscale Young's modulus of biofilms produced by Shewanella oneidensis MR-1 in a liquid phase. The indentation test was performed on a biofilm sample using the atomic force microscopy (AFM) with a spherical indentor, and the force-indentation responses were obtained during approach and retraction traces. Young's modulus of biofilms was estimated to be similar to 33-38 kPa from these force-indentation curves and Hertzian contact theory. It appears that the AFM indentation result captures the microscale local characteristics of biofilms and its stiffness is relatively large compared to the other methods, including rheometer and hydrodynamic shear tests, which reflect the average macro-scale behaviors. While modeling of mechanical behaviors of biofilm-associated soils requires the properties of each component, the obtained results provide information on the mechanical properties of biofilms that can be considered as cementing, gluing, or filling materials in soils.