FDTD (Finite-Difference Time-Domain) method has been widely used for the analysis of photonic devices consisting of sub-wavelength structures. In recent years, increasing efforts have been made to implement the FDTD on GPGPUs (General-Purpose Graphic Processing Units), to shorten simulation time. On the other hand, it is widely recognized that most of the middle- and low-end GPGPUs have difference of computational performance, between single-precision and double-precision type arithmetics. Therefore the type selection of single/double precision for electromagnetic field variables in FDTD becomes a key issue from the viewpoint of the total simulation performance. In this study we investigated the difference of results between the use of single-precision and double-precision. As a most fundamental sub-wavelength photonic structure, we focused on an alternating multilayer (one dimensional periodic structure). Obtained results indicate that significant difference appears for the amplitudes of higher order spatial harmonic waves.