Edible oil is chief import of Pakistan. To overcome this problem, improved cultivars requirement can not be over-emphasized. To achieve this goal, estimation of genetic diversity has great value for a crop breeder for improving the crop and producing high yielding varieties. In present studies, 114 accessions of Brassica campestris L. and 25 accessions of Brassica napus L. were evaluated for 15 agro- morphological and 6 seed quality traits for two years 2004-05 and 2005-06. Seed storage proteins profile of all the accessions was estimated using SDS-PAGE. Accessions with desirable traits were identified for exploitation in breeding program. A six parent diallel was carried out to study inheritance mechanism of 15 agro- morphological and 6 seed quality traits in Brassica napus L. Among the accessions of Brassica campestris L., high variance was observed for number of siliqua per plant followed by seed yield per plant, plant height, days to flower initiation, number of siliqua per main inflorescence and glucosinolates content. Significant positive association of seed yield with number of siliqua per main inflorescence and number of siliqua per plant suggested that these traits are yield contributing traits and must be selected for yield improvement. Cluster analysis distributed the accessions into six clusters during 2005 and into five clusters during 2006. It was found that 7 and 5 principal components (PCs) with eigen values > 1 contributed 74.09% and 66.08% of total variation during 2005 and 2006, respectively. Similarly, among Brassica napus L. accessions, high variance was also shown by number of siliqua per plant, plant height, seed yield per plant, glucosinolates, number of siliqua per main inflorescence, length of main inflorescence and oleic acid content. Significant positive association of seed yield with number of siliqua per main inflorescence and siliqua per plant revealed that these traits are really yield contributing traits and must be selected in an effective breeding program for yield improvement. Accessions were distributed into five clusters by cluster analysis during 2005 and into four clusters during 2006. Genetic variability was also studied using principal component analysis and variables were considered simultaneously. It was 12 found that 7 and 5 of 21 principal components with an eigen value higher than 1.0 exhibited 84.75% and 80.16% of the total variation during 2005 and 2006, respectively. All the 114 accessions of Brassica campestris L. were used for sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) analysis. In total, 16 polypeptide bands were observed. Out of 16 protein bands, 12 (75%) were polymorphic and 4 bands (25%) were monomorphic. Close relationship was observed among most of the accessions except few. Total seed proteins of all the 25 accessions of Brassica napus L. were analyzed using sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). In total, 17 polypeptide bands were observed. Out of 17 protein bands, 10 (59%) were polymorphic and 7 bands (41%) was monomorphic. Close relationship was observed among most of the accessions. Inheritance studies in Brassica napus L. were carried out following Hayman , s Approach (Hayman, 1954 a) as advocated by Singh and Chaudhry (2004). Additive as well as non additive variances were observed for yield and yield related traits. Over dominance was observered for all characters except days to flower initiation, days to flower completion and days to maturity. In conclusion, germplasm exhibited wide genetic diversity for the studied traits. Accessions with desirable traits (early maturity, higher yield potential, higher oil content and low in erucic acid and gloucosinolates) were identified which can be used for rapeseed improvement. Over dominance with additive as well as non additive variance was found for most of the traits indicating the selection in later segregating generation.