Abstract: Six canola (Brassica napus) varieties were used in this study which was chosen as a representative sample of commercial canola varieties used for oil production. The objectives of this study were; 1) cluster the varieties understudy using the morphological characters oil and protein percentages, 2) estimation the genetic diversity among varieties understudy using RAPD markers, and 3) find the correlation between RAPD and morphological diversity. Data showed that the averages of all varieties for oil and protein percentages were 39.38 and 16.77, respectively. Euclidean distances based on oil and protein percentages were calculated. Their values ranged from 14.14 to 92.05 and the average of the distances was 42.9. This data indicated that the amount of phenotypic variation among the varieties was relatively high. The cluster diagram based on Euclidean distance separated varieties into two groups. Also, data of the 10 random primers used indicated a total of 401 scorable bands. Total amplified DNA fragments were 93 and number of DNA fragments per primer varied from 6-13. Total polymorphic fragments were 55 with an average of 57.76% polymorphic fragment per primer. The similarity coefficient values based on RAPD markers ranged from 0.114 to 0.261 with an average of 0.183. The conducted dendogram showed that five varieties formed one main cluster. RAPD results (81.7% divergence) indicated higher diversity than indicated by oil and protein morphological markers (42.9%). Finally, Mantel test was calculated to find out the correlation between RAPD markers and morphological characters matrices. A lack of correlation was obtained (r = -0.08992) and many possible reasons were discussed.