Saffron is very appreciated as a spice, as a product for therapeutic use and as a natural coloring. It consists of the dried stigmas of the flower of Crocus sativus L., an iridaceae with corms. Its exorbitant price of up to $30/g frequently exposes it to fraud and requires the use of effective controlling methods to guarantee its authentication. The pruning of saffron flowers generates waste at the rate of 350 kg per kg of stigmas. This waste is discarded without any recovery. T he use of molecular markers such as SSRs and ISSRs is undertaken with the objective of finding a molecular identity of saffron from different countries and those of accessions belonging to the same country to distinguish them and trace the exact origin of saffron. T he search for SSRs at the level of the available genomic sequences of C. sativus made it possible to identify 26 pairs of primers which are used for the PCR amplification of 12 accessions of Moroccan saffron originating from the regions of Taliouine (province of Taroudant) and from Taznakht (province of Ouarzazate) and Greek and French saffron. These saffron samples are also used as a template for the PCR amplification of 10 ISSRs. T he data analysis made it possible to obtain a polymorphism of 40.38% despite the mode of vegetative propagation of this species, to clearly distinguish by these molecular markers, French saffron and certain Moroccan accessions and to draw up a dendrogram for the studied genotypes. T he use of the pruned saffron flowers for the production of bio-dye has involved aqueous extraction and treatments with different combinations of concentrations, temperatures, pH and dye times on cotton and wool. The parameters followed concern color yield, fastness to washing, dry and wet friction, acid and alkaline perspiration and light stability. It emerges from this study that the dyeing of wool and cotton by the extract of the petals of saffron flower is better with a concentration of 10% of dye, an acid pH (pH = 3) of the bath, a temperature of 90 ° for wool and 98 ° for cotton, for one hour. The dye is well fixed by wool than by cotton. The use of mordants increases wash resistance. It accentuates the coloring with only 3% of the dye and made it possible to obtain a wide range of colored tints from yellow to brown and green which shows that saffron petals waste can be a good natural dye for the cotton and wool textile industry. Key words: Saffron, Crocus sativus L., Molecular markers, Flowers waste, Bio-dye.