The gene duplication rate in the yeast genome is estimated without assuming the molecular clock model to be ∼0.01 to 0.06 per gene per billion years; this rate is two orders of magnitude lower than a previous estimate based on the molecular clock model. This difference is explained by extensive concerted evolution via gene conversion between duplicated genes, which violates the assumption of the molecular clock in the analyses of duplicated genes. The average length of the period of concerted evolution and the gene conversion rate are estimated to be ∼25 million years and ∼28 times the mutation rate, respectively.