The time-series normalized difference vegetation index (NDVI) product has proven to be a powerful tool to investigate the phenological information because it can monitor the change of the forests with very high time-resolution, This study described the application of the DFT analysis over the 9 year MODIS data for the identification of the two types of vegetation cover, Pinus densiflora(Pd) and Querqus mongolica(Qm) which are dominant species of evergreen and broadleaved deciduous forest, respectively, The total number of samples was 5148 reference cycles which consist of 2160 Pd and 2988 Qm. They were extracted from the pixel-based MODIS scenes over the 9 years from 2000 to 2008 of South Korea. The DFT analysis was mainly focused on the 0th and $1^{st}$ harmonic components, each of which represents the mean value and the variation amplitude of the NDVI over the years, respectively. The $0^{th}$ harmonic values of the vegetation Pd and Qm averaged over the 9 years were 0.74 and 0.65, respectively. This implies that Pd has a higher NDVI than Qm. Similarly obtained $1^{st}$ harmonic values of Pd and Qm were 0.19 and 0.27, respectively. This can be intuitively understood considering that the seasonal variation of Qm is much larger than Pd. This distinctive difference of the $1^{st}$ harmonic value has been used to identify evergreen and deciduous forests. Overall agreement between the Fourier analysis-based map and the actal vegetation map has been estimated to be as high as 75%. This study found that the DFT analysis can be a concise and repeatable method to separate and trace the changes of evergreen and deciduous forest using the annual NDVI cycles.