Genome sizes vary widely across the tree of life and the evolutionary mechanism underlined remains largely unknown. Lynch and Conery (2003) proposed that evolution of genome complexity was driven mainly by nonadaptive stochastic forces and presented the observation that genome size was negatively correlated with effective population size (Ne) as a strong support for their hypothesis. Here, we analyzed the relation between Ne and genome size for 10 diploid Oryza species that showed about fourfold genome size variation. Using sequences of more than 20 nuclear genes, we estimated Ne for each species after correction for the effects of demography and heterogeneity of mutation rates among loci and species. Pairwise comparisons and correlation analyses did not detect a negative relationship between Ne and genome size despite about 6.5-fold interspecies Ne variation. By calculating phylogenetically independent contrasts (PICs) for Ne, we repeated correlation analysis and did not find any correlation between Ne and genome size. These observations suggest that the genome size variation in the Oryza species cannot be explained simply by the effect of effective population size.