Crop production is significantly limited by waterlogging especially in high rainfall and poorly drained regions in the world. Hence, breeding for waterlogging tolerance to increase production is one of the main objectives of breeders. Similar to other abiotic stress tolerances, the tolerance to waterlogging is a complex trait and difficult to select for in breeding programs. Marker assisted selection has been an effective method for crop improvement by utilizing markers closely related to target traits combined with accurate phenotyping of key factors. In the present study, two bread wheat (Triticum aestivum L.) F-2:3 populations ('Dogankent' x 'Ducula-4' and 'Ducula-1' x 'Seri-82') derived from susceptible cultivars ('Dogankent' and 'Seri-82') and tolerant ('Ducula-1' and 'Ducula-4') lines were treated with four weeks of waterlogging and screened in two different locations. Additionally, 32 expressed sequence tags and 210 microsatellite markers were screened for analysis of marker trait associations; of which less than %20 (45) of those markers were polymorphic between parents of both populations. Tolerance, yield and quality related traits including plant height index, tillering index, adventitious root formation, heading date, tolerance scoring index, total kernel number and thousand kernel weight were identified to be mostly affected by environment. Marker - trait analyses identified markers significantly associated with waterlogging tolerance as well as yield and quality component traits. In the 'Dogankent' x `Ducula-4' derived population, two markers explaining more than 10% of the total variance for adventitious root formation and thousand kernel weight were detected both on chromosomes 3DL (Xgwm645) and 4AL (Xgwm160). This is one of the first studies revealing markers linked to the tolerance related traits in spring wheat under waterlogging conditions.