A multi-tool analytical practice was used for characterization of 16^th century carpet manufactured in Cairo. Mild extraction method with hydrofluoric acid enabled isolation of intact flavonoids and their glycosides, anthraquinones, tannins and indigoids from fibre samples. High-performance liquid chromatography coupled to spectroscopic and mass spectrometric detectors was used for identification of natural dyes present in the historical samples. Weld, young fustic and brazilwood were identified as the dye sources in yellow thread samples. Red fibres have been colored with lac dye, whereas green fibre shades were obtained with indigo and weld. Tannin-containing plant material in combination with indigo and weld were used to obtain brown hue of thread. Four uncommon and thus-far unknown dye components were also found in the historical samples. These compounds probably represent unique fingerprint of dyed threads from this region. Scanning electron microscopy with energy-dispersive X-ray detector (SEM-EDS) and Fourier transformation infrared spectroscopy (FT-IR) were used for identification and characterization of substrates and mordants present in the historical carpet. Carbon and oxygen were detected in large quantities as a part of the wool protein. The presence of aluminum, iron and calcium indicated their usage as mordants. FT-IR analysis showed bands characteristic to woolen fibres and SEM micrographs definite structure of wool.