In this numerical study, natural frequency analysis of the layered functionally graded beams in the thickness direction for clamped-clamped and clamped-free boundary conditions was investigated using finite element software ANSYS and the effects of the layers on natural frequency analysis for first mode were evaluated under clamped-free boundary condition. The layer arrangements of the beams were performed according to Taguchi L9 (3x3) orthogonal array. Mechanical properties of the layers made of different volume fractions of Ti-6Al-4V and ZrO2 materials was assumed as control factors. In order to determine the optimum layers and their levels, signal-to-noise (S/N) ratio analysis was used. Significant layers and their percent contributions on the first mode natural frequency were carried out using Analysis of Variance (ANOVA). In addition, the effects of the boundary conditions (B.C.) such as clamped-free (C-F) and clamped-clamped (C-C) and positions of the optimum layers were evaluated. According to results observed, maximum first mode natural frequency for C-F boundary condition using optimum layers were found using the FG beams with top and bottom layers with ceramic-rich and middle layer with metalrich. The most effective layers on the responses was obtained as L1 with 48.4523%, L2 with 16.1547% and L3 with 34.9839%. Layer arrangements for C-F boundary condition play important role on the natural first mode frequency.