Microorganisms cause various types of damages to timber such as decay, soft rot, mould, stain and bacterial degradation. Of these, moulds and stains are common on rubber wood. The predominant fungus causing sapstain in rubber wood is Botryodiplodia theobromase. Due to the environmental conditions favourable to fungal growth, sapstain is a serious problem to the utilization of rubber wood in Kerala. A detailed study on the factors affecting the growth and colonization of B.theobromae was carried out. The study revealed that no growth of B.theobromae occurred at and below 23.8 per cent moisture content of rubber wood. Moisture content of 29.0 per cent and above was most favourable for heavy growth of the fungus on Potato Dextrose Agar medium. The results indicated that once B.theobromae was established in the wood. Moisture content of 29.0 per cent and above was most favourable for heavy growth of the fungus on Potato Dextrose Agar medium. The results indicated that once B. theobromae was established in the wood, the mycelium was not killed on the surface as well as inside the wood at 50 degree C even after 7 days of incubation. The weight loss of rubber wood due to the infection by B.theodermae was studied and it was found that the weight loss in the first month was 8.0 per cent which increased to 12.2 per cent at the end of fourth month. But in Alstonia scholaris, the weight loss accounted was 4.5 per cent at the end of fourth month. Density of stained rubber wood was determined and it was seen that there was a reduction in the end of fourth month. No reduction in the compressive strength of stained wood was noted whereas the bending strength was reduced when compared to unstained wood. In the field evaluation of different chemicals/fungicides for the control of sapstain and decay, Captafol even at 3 per cent did not prevent mould and sapstain completely on rubber wood. When open and close stacking were compared, better control was achieved by open stacking. Busan 1009 in combination with boric acid was effective in controlling fungal growth. Hylite extra and chlorothalonil were found to be equally good in controlling sapstain. Chlorothalonil at 1 per cent was found to be effective in controlling sapstain. During rainy season, the concentration of the fungicide has to be increased for better control of fungal growth.