This work presents an application of the evolutionary structural optimization (ESO) method to optimize two of the most common bonded joints - the single lap joint and the double lap joint. The ESO method was used to shape the adherends contour to reduce peak stresses at the overlap ends. The shape optimization was performed under a von Mises rejection criterion. The von Mises stress was evaluated using the finite element model for both types of joints. It is proposed here to utilize a honeycomb-like mesh using hexagonal elements to minimize stress concentration problem. Additionally, the use of a honeycomb mesh in the ESO method led to a smoother adherend contour. Numerical results show how the stress distributions for both shear and peel stresses are improved after the application of this optimization method.