Synthetic dyestuffs released by the textile industry pose a threat to environmental safety. Textile effluent always contains some unreacted dyes from dyeing processes. Beside of giving undesired colour to water, these dye molecules prevent sunlight scattering so interrupt photo synthesis reaction and lead to reduction of dissolved oxygen in the water. Treatments of vat dye effluents have a great importance because of their highly complex chemical structure and their water insolubility which cause serious environmental problems. Treatment of effluents generally can be categorized in physical, chemical and biological methods. Biological methods have several benefits like environmental friendly process, economical, producing less sludge and less water consumption. In this research, decolourization ability of a fungi strain ( Aspergillus niger ) for eliminating 10 vat dyes, 1 acidic and 1 disperse dye with different molecule structures was investigated. Decolourization carried out in two ways; pre-growth fungi and simultaneous growth and decolourization. Effect of molecular weight, side groups, and sterochemical structure of dyes on absorption capacity of fungi and rate of decolourization was investigated. Results showed that, absorption percentage and absorption rate was higher for molecules with planner structure. Dyes with higher molecular weight showed higher absorption rate. Also dyes with NH and NH 2 functional groups in the structure exhibited slow adsorption due to their affinity toward water. Furthermore, dye adsorption by fungi in real dyeing conditions in different pHs was studied also. Results showed that alkaline media prevent fungi grow. In another approach, fungi dried body mass namely dead sludge was used for dye removal. This method showed lower efficiency than other methods. Fourier Transform Infrared spectroscopy was applied to confirm the existence of hydrogen bonding between dye and fungi in addition to vanderwaals forces as absorption mechanism. Keywords: Wastewater, Vat dyes, Aspergillus niger, FTIR