This study aimed to analyze chemical changes by Fourier Transform Infrared Spectroscopy of Eucalyptus dunnii and Pinus elliottii treated woods subjected to an accelerated decay test with the white rot fungus Ganoderma applanatum. The wood test specimens (2,5x2,5x0,9 cm) were impregnated with preservative solutions of chromated copper borate and synthetic pyrethroids and carbamates with 6% concentration by a vaccum-pressure process. After a decay test of 16 weeks, the chemical changes of the treated and untreated wood samples were evaluated by Fourier Transform Infrared Spectroscopy. It was observed that the rot fungus attack caused a variation in the intensity and a displacement of spectrum peaks, indicating a change to the woods' chemical composition after fungal exposure. The lignin / carbohydrate ratio indicated that the fungus had no preference for a specific cell wall component, pointing to a simultaneous deterioration of cellulose, hemicellulose and lignin in the treated and untreated woods. Finally, the Fourier Transform Infrared Spectroscopy technique, together with the lignin / carbohydrate ratio analysis, proved efficient in the study of the variation of the wood chemical modifications deteriorated by rot fungi. Universidad del B í o -B í o Maderas. Ciencia y tecnología 20(3): 479 -488, 2018 Universidad del B í o -B í o Maderas. Ciencia y tecnología 20(3): 479 -488, 2018According to Costa et al. (2011), the decrease of the lignin / carbohydrate ratio is due to a preference of the rot fungus to deteriorate the lignin at a higher rate, in detriment of the other components, such as cellulose and hemicellulose.However, in the present study, it was verified that the ratios showed a reduction and an increase in their values, possibly indicating a simultaneous deterioration of the chemical compounds of the wood, which corroborates with Schmidt (2006) and Pandey and Nagveni (2007), who highlight that in simultaneous white rot fungi, lignin and carbohydrates are removed at a similar rate, causing a homogeneous deterioration of the wood.