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The different parts ofAzadirachta indica has significant medicinal values in Ayurveda field. They are commercially used for synthesis of different therapeutic drugs in pharmaceutical sector. In this study, dried flowers of Azadirachta indica RUBL21378 has been used for synthesis of natural dye. The phytochemical screening was performed in different extract of their dried flower in organic solvents like methanol, ethanol, and acetone. These phytochemical screening had confirmed the presence of different bioactive components like saponins, quinone, flavonoids, and alkaloids. They showed specific antimicrobial property with effective zone of inhibition 0.5mm and 16mm against Escherichia coli and Staphylococcus aureus respectively. Copper sulphate was added as mordant during incubation period of dying process of cotton fabrics with flower extract. These fabrics exhibited a significant level of natural dye absorption at 50°C after incubation period up to 3 hours. The colour fastness was observed after treating them with sunlight at different interval of time period for 24, 48, and 72 hours. These fabrics showed stability in detergent solution (2%) for 30 minutes at 50°C. These fabrics showed equal colour intensity after dyeing with green tea as mordant. Their color intensity was increased after dyeing with flower extract of Acacia catechu as bio mordants. The functional groups are investigated by FTIR spectrum analysis. This methodology for synthesis of natural dyes could be efficiently employed in textile industry for colouring cotton fabrics at large scale.