The present study was carried out to identify the best cross(es) for Orobanche tolerance using genetic variance components and molecular analyses among four parents of faba bean, their six F₁ crosses and six F₂ populations which were produced via half-diallel mating design under Orobanche infected soil condition. Significant mean squares were recorded for parents and crosses for the studied traits. The GCA/SCA ratio was higher than unity for all studied traits, except for number of Orobanche spikes/plant and 100-seed weight. Highly significant positive and negative correlation coefficients were obtained among almost studied traits. Broad sense heritability ranged from intermediate to high and from low to intermediate for narrow sense. Five RAPD and five SSR primers were used for marker-assisted selection for Orobanche tolerance in parents and their F₂ populations. In the case of RAPD primers, three of them showed higher resolving power (RP) rates and were found to be more suitable for genetic diversity analysis in the genotypes under study. In the case of SSR markers, the average value of resolving power was 5.24 per primer. Moreover, primer GA4 was found to be the most suitable for genetic diversity analysis among genotypes under study while, it recorded the highest RP value (7.64). The average values of polymorphic information content were 0.27 and 0.34 per primer based on RAPD and SSR data, respectively. The molecular distance among four faba bean parents and their F₂ bulks ranged from 0.099 to 0.556 by using RAPD and SSR combined data. Positive genotype-specific markers were recorded in some genotypes with molecular sizes ranged from 180 bp to 1584 bp by using both DNA markers. These positive specific markers may play important roles in Orobanche tolerance in faba bean.