Pakistani Bread wheat (Triticum aestivum) germplasm consisting of 204 land races belonging to different parts of Pakistan were characterized for phenological pa rameters, disease resistance against stripe rust (Yr) and Karnal bunt (KB), seed struc ture and high molecular weight glutenin subunits. Only one landrace form Dir was re sistant to KB with less than 1% bunted grains. Four landraces were found to be resistant to Yr and moderately sensitive to KB. A positive correlation was found between tillers per plants, plant height, spikelet/spike, grain/spike, TKW and grain yield. Cluster anal ysis divided landraces into seven groups on the basis of morphological similarities. Not all landraces in a cluster belonged to the same geographical origin. A high throughput analysis based on digital imaging was carried out to find the association between grain size, shape and thousand kernel weight (TKW) in Pakistani wheat landraces using PCA and multiple regression. It was revealed that grain thickness has a maximum and direct effect on grain weight. Grain weight is less effected by horizontal area of seed. A total of forty-two different allelic combinations were found for HMW-GS. Higher frequency of Null and 2+12 were observed in this germplasm. The most frequent allelic combination was 2*, 17+18, 2+12 in 25 landraces. Allelic diversity at Glu-1 revealed that Glu-BI is the most diverse locus. Quality score ranged between 4-10, with 33 land races having the highest score of 10. xviii Functional markers were applied to detect various genes related to agronomic traits, quality and disease resistance. These markers have identified a large number of these landraces to have increased height, photoperiod insensitivity, spring habit, lower TKW, lower spike number and decreased yellow pigment content. Favourable alleles associated with drought resistance were present in higher frequencies. Genotyping by sequencing (GBS) was also conducted to understand the genetics of complex traits in these landraces. Awn length was found to be associated with genomic regions on 3B, 1D, 3D, 6A and 7A and plant height on 1D. Highest MTAs were detected for spike length on chromosome 1A, 1B, 2B, 2D, 4B, 5B, 6A, 6B, 7A and 3A. Grain per spike was found to be associated with four linked and one unlinked marker. Marker S2AL_U_919434 explained 22% of phenotypic variation and grain per spike was found to be associated with TKW.