Two varieties V2 and V12 and their descendents of Nicotiana rustica were used to create four artificial different cycles of random mating populations. The effect of linkage disequilibrium on generation mean and variance was explored theoretically and practically on the two of character flowering time (FT) and final height (FH). Results showed that evidence of linkage was found in mean and variance levels and the variance of both additive and dominance became smaller as the cycles of random mating increased. This is the evidence of coupling linkage. The effects of intensity of linkage and the degree of association of genes on generation mean and variance were also discussed in the paper.