Identification of soil components and soil organic matter characterization by functional group differentiation are the important applications of Fourier transform infrared spectroscopy (FTIR). Study intended to identify the FTIR spectra of changes in the carbon functional groups by the growth of rubber seedlings in three different pH and base cation soils between initial and after 240 days. Weighed, sieved soil samples powered in an agate mill were homogenized and mixed KBr (FT-IR grade) and the pellets were made using a hydraulic press at 12 bar, dried FTIR Spectra recorded with a Spectrophotometer (Varian 660 – IR FTIR) with specified resolution. Results indicated that the spectrum of all three soils comprised of the clay mineral (left portion) organic matter (middle portion) and minerals (right portion) in the peaks obtained in three soils. The spectrum of the two acidic soil (pH 4.4 and pH 5.5) were similar and these were different from the neutral soil (pH 7.4). In pH 4.4 and pH 5.5, 6 peaks in the left portion were similar. This corresponds to the clay minerals and naturally these were identical in the acidic soils dominated in Kaolinite clay mineral. But in pH 7.4 among the 6 peaks two were present and instead of other peaks there was a broad peak corresponds to the centre point at intensity of 3400 cm-1associated with the hydrogen bonding with the functional group OH and it is a determining factor of the presence of exchangeable cations like K, Na, Ca and Mg. This was the confirmation of the characteristic difference in pH 7.4 soil from pH 4.4 and FTIR spectrum is applicable in identification of soil differentiation by carbon groups.