Egypt, with its growing population, suffers from a lack of self-sufficiency in important food crops such as wheat and depends on imports from abroad. Therefore, we urgently need to develop agriculture and introduce new crops that help reduce the food gap. Quinoa is a promising new crop introduced to Egypt through the few past years. Molecular and biochemical markers were used to identify the level of polymorphism and to study the genetic relationships among quinoa genotypes. Ten quinoa genotypes characterized by using ten genetic molecular primers (five ISSR and five SRAP markers) as well as protein electrophoresis pattern. The genetic polymorphism analysis revealed that the 10 primers combinations successfully amplified and generated 138 bands of which 88 (64%), were polymorphic across the 10 genotypes. The PIC values for ISSR and SRAP primers combination varied from 0.23 to 0.21 respectively, with an average of 0.22. The general average of MI values was 1.99 for ISSR and SRAP. While, general average of resolving power (RP) was 4.4% for all primer's combinations. Nei and Li/Dices similarity coefficients ranged from 0.75 to 0.91 for ISSR and SRAP primers combinations. Also, protein electrophoresis showed seven common bands among the ten quinoa genotypes. Egyptian and Black genotypes revealed unique bands at the molecular weights 58 and 44 kDa, respectively. Finally, five polymorphic protein bands produced 42% of polymorphism. Obtained results indicated that molecular and biochemical markers techniques are useful in the establishment of the genetic fingerprinting and estimation of genetic relationships among quinoa genotypes.