Linen is the most historical Egyptian textile fibre liable to fungal deterioration. Fungal deterioration of dyed linen textiles may appear as undesirable different stains. In order to success in removing of fungal stains from biodeteriorated historical Egyptian dyed linen textiles, it is necessary to understand the nature and causes of these stains, hence their subsequent removal. So this paper aims to investigate the effect of fungi on dyed linen textiles. In this study linen textile samples were experimentally dyed by two different dyes, blue one as an example to vat dye and yellow one as an example to direct dye. This work is done on two of the most important dyes (Turmeric and indigo), which were popular in most of historical periods in Egypt. Dyed linen samples were experimentally biodegraded by thirty different fungal strains isolated previously from historical Egyptian linen samples. The produced change in colours of the biodeteriorated samples was detected visually. Also, the change in reflection spectra and colour differences produced to dyed linen textiles after fungal deterioration, were assessed and evaluated by using spectrophotometer. This study reported that most of tested fungi contribute to discoloration of all tested dyed linen samples. These results indicate that most of stains on historical Egyptian dyed linen textiles, may be fungal stains. The results confirm that undyed linen textiles more liable to fungal biodeterioration than dyed ones. Also the results show that yellow dyed linen textiles are more susceptible to fungal deterioration than blue dyed linen textiles. The obtained results show that Alternaria tenuissima, Chaetomium globosum, Chaetomium sp., Penicillium raistrickii, P. soppi, P. asperum, P. citrinum, Aspergillus carbonarius, A. fischeri, A. nidulans, A. terreus and A. niger, had showed the maximum colour changes of the deteriorated yellow dyed linen samples. The results also show that Alternaria tenuissima, Chaetomium sp., Penicillium asperum, P. citrinum, Aspergillus nidulans and A. spinulosus, had shown the maximum colour changes of the deteriorated blue dyed linen samples.