Faba bean (Vicia faba L.)(V. faba), an essential legume in Egypt, is severely impacted by broomrape (Orobanche crenata) (O. crenata), a parasitic weed that feeds on roots, making chemical control difficult without harming the crop. Three faba bean genotypes (Giza-843, Misr-3, and Sakha-3) along with nine pure lines were evaluated for resistance to broomrape in field trials (2021–2023) using gene barcoding (rbcL, rpoC1), ten Start Codon Targeted (SCoT) markers, and phonological and agronomic traits to identify resistance sources. Five faba bean genotypes—Giza 843, Lines 2, 7, 8, and 9— significantly reduced all broomrape growth and productivity traits. Line 5 had the lowest spike length, fresh and dry spike weight, number of spikes/m2, and number of capsules/spike across both seasons. Genotypes Line 5, Line 6, and Misr 3 exhibited the highest seed yield per plot and hectare under normal and broomrape-infested conditions. Line 4 showed the lowest yield reductions, followed by Lines 9 and 8. The study generated 103 amplicons with a polymorphism rate of 51.46%, with SCoT-10 being the most informative marker, revealing 69% polymorphism and affecting 13 amplicons. Three faba bean genotypes showed significant genetic diversity, high seed output, and effectively reduced broomrape growth, highlighting their potential for genetic improvement and sustainable use in future research. Four faba bean genotypes, namely Sakha 3, Line 2, Line 4, and Line 9, are promising genotypes for combating broomrape infestation.