Kenaf and luffa fibres are hydrophilic due to the presence of water sensitive constituents, which tend to form a poor compatibility when binding with polymers. Thus, the surface of fibres was modified through fungal, alkaline and heat treatment to reduce the main hydroxyl functional groups (O-H) that caused the water absorption as well as to cleave the formed hydrogen bonds that hindered the compatibility. The samples were treated with Phanerochaete Chrysosporium (PC) and Fusarium Oxysporum fungi separately for 5, 10 and 15 days. Furthermore, the samples were alkaline treated with 5 wt% of sodium hydroxide at increased temperature of 25 degrees C, 50 degrees C, 70 degrees C and 90 degrees C, where it showed improvement in the hydrogen bond removal rate. Moreover, the samples that heat treated under higher temperatures of 120 degrees C, 140 degrees C, 160 degrees C and 180 degrees C were found to have the lower cellulose and hemicellulose contents due the evaporation of water molecules. Generally, through Fourier transform infrared spectroscopy analysis, both the fibres treated with PC fungi had the lowest O-H content due to the detection of the largest reduction of the O-H stretching band intensity compared to others. Furthermore, the highest weight loss and the lowest water absorption percentages were also detected from these fibres, which also indicated the good modification between the fibres and the PC fungi. Therefore, the fungal treatment using PC fungi is the most effective and environmentally friendly method to improve the fibres' hydrophobic property.