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Wheat (Triticum aestivum L.) rusts are the most widespread and destructive among all other diseases of wheat because of their wide distribution, and their capacity to form new races that can attack previously resistant cultivars which result in serious yield losses. Stem rust caused by Puccinia graminis f. sp. tritici and leaf of orange rust caused by Puccinia recondita are more effective and durable when several rust resistance genes are pyramided into a single line. Molecular survey was conducted to screen altogether 44 Pakistani wheat germplasm lines consisted of 23 cultivated varieties for the presence of Lr10 and Sr9a genes by using co-dominant STS and SSR primers specific for respective alleles. The polymorphic survey revealed that out of 44 germplasm lines obtained from Ayub Agriculture Research Institute, 31 genotypes were observed with Lr10 gene (including C-228, C-245, C- 288), while 13 germplasm lines did not show the presence of Lr10 gene. Of the 23 cultivated varieties, 21 varieties observed Lr10 gene (including Auqab 2000, Chenab-70, Punjab-76, Kohsar-95, Parvaz-94, Pasban-90, Chenab-2000, Satluj-86, Shahkar-95), while only Kohsar 95 and PARI 73 did not show the presence of Lr10 gene. Molecular survey for Sr9a gene depicts that 33 genotypes were observed for stem rust resistance like C-248, LR26, C-250, C-271, C-273, C-288 and C-518, while 11 genotypes (including C-228, C-245, C-247 and C-271) showed no such fragment. Of 23 conventional cultivated varieties, 21 varieties showed the presence of Sr9a stem rust resistance gene like Punjab-76, Pak-81, Kohistan-97, Kohsar-95, Parvaz-94, Pasban-90 etc and 4 varieties showed the absence of Sr9a stem rust resistance gene like Shahkar-95, Parvaz-94, Chenab-2000 and Chenab-79. The identification of Lr10 and Sr9a in Pakistani wheat germplasm will help in accelerating the breeding program in future, including pyramiding of different wheat resistant genes in wheat varieties.