Whole genome duplication (WGD) in plant lineages can be associated with shifts in flowering time, which, if sufficiently large, can promote the establishment of polyploid species. However, the influence of genotype and the underlying patterns of gene expression on variation in the effects of WGD are poorly understood. I examined the impact of WGD on flowering time for 45 diploid genotypes of Arabidopsis thaliana in a common environment and compared gene expression of five flowering time genes, FLC, CO, FT, FRI, GAI, in a subset of genotypes exhibiting either small or large WGD effects. On average, WGD increased time to flowering but the magnitude of effect differed significantly among genotypes from 0 to 51%. Based on eight accessions, there were no differences in mean expression between diploid and tetraploid cytotypes for any flowering time gene. However, the expression of FLC, CO, FT and GAI differed significantly between genotypes exhibiting small versus large WGD effects on flowering time. Furthermore, post-hoc means comparisons for FLC and FT showed a significant difference in expression between tetraploids of small vs large WGD effects groups. Lastly, the different effects of WGD on flowering time were eliminated after vernalization. Collectively, these data suggest that the effects of WGD on flowering time are highly-genotype specific and that gene expression is not uniformly affected by WGD.