Molecular markers are important tools in plant genome analysis and became as a useful tool in crop improvement. It facilitates the identification of markers for agronomical important traits and for genetic and genomic characterization. The current study aims at the identification of the genetic diversity and relationship, as well as the evaluation of the productively of five Triticale genotypes, namely; ICBA 2, Triticale 8, 11, 7 and 6, imported from ICBA "International Center for Biosaline Agriculture" Dubai, Arab Emirates to perform genetic and productivity evaluationunder North Sinai conditions. The study was performed at Baloza Research Station, Desert Research Center, in 2016-2017 and 2017-2018 seasons.Two molecular markers; ISSR and SCoT target different regions of DNA were used for genetic studies. Twelve ISSR and SCoT molecular markers were selected from 25 markers, which produced clear bands were selected. The six ISSR primers produced 78 amplified fragments, 30 of them were polymorphic, representing around 38.5%. The ISSR markers similarity matrix ranged from 81 to 92%, where the highest similarity matrix was between Triticale 8, 7 and 8, 6.  The lowest similarity was between Triticale 11 and 7. The SCoT primers produced a total of 89 amplified fragments, where 28 of them were polymorphic, representing about 31.5% of polymorphism. The SCoT markers similarity matrix ranged from 94 to 85%. The highest similarity matrix was between Triticale 8, 7 and 8, 6, too. The dendrograms based on ISSR, SCoT and both of them were attended, the total polymorphism was 34.7% with PIC value of 0.9415. Triticale 11 and ICBA 2 were the most distinguished genotypes. The results showed that both ISSR and SCoT markers were efficient for analyzing genotypes.The productivity results revealed that Triticale 11 had the highest values in yield components as well as the other studied characters, while the lowest values were restricted to Triticale 6 in both studied seasons. According to the studied yield component characters (grain, straw and biological yield as kg/feddan),Triticale genotypescan be arranged in descending order as T. 11, ICBA 2, T. 8, T. 7 and T. 6, that have the highest value to the lowest in the two seasons.