During the last few decades, the requirements for modern machine elements in terms of size reduction, increasing the energy efficiency, and a higher load capacity of standard and non-standard gears have been very prevalent issues. Within these demands, the main goals are the optimization of the gears’ tooth profiles, as well as the investigation of new tooth profile designs. The presented design idea is based on the optimal solutions inspired by nature. Special attention is paid to the new design of the tooth root zones of spur gears in order to decrease the stress concentration values and increase the tooth root fatigue resistance. The finite element method is used for stress and strain state calculations, and the particular gear pair is modeled and optimized for these purposes. For tooth root strength analysis, the estimations are based on the theory of critical distances and the stress gradients obtained through finite element analysis. The obtained stress gradients have shown important improvements in the stress distribution in the transition zone optimized by biomimetics. An analysis of the material variation influence is also performed. Based on the investigations of a particular gear pair, a significant stress reduction of about 7% for steel gears and about 10.3% for cast iron gears is obtained for tooth roots optimized by bio-inspired design.