To reveal the relationship between organismal evolution and the molecular evolutionary rate, the temporal pattern of evolutionary rates were investigated for various genes during the course of deuterostome evolution. Deuterostome lineage leading to extant mammals was tentatively divided into two periods (the First and the Latter periods) by the time of divergence of bony fishes and mammals. For each of the First and the Latter period, evolutionary rates of 207 gene sets were calculated. In the Latter period, the evolutionary rate was significantly reduced in such informational genes as transcription factors and cytoplasmic ribosomal RNAs and proteins. In contrast, a variety of enzymes and mitochondrial ribosomal proteins evolve at nearly constant rate throughout the First and the Latter periods. The present result suggests that the increase of gene number by extensive gene duplications in the early evolution of vertebrates is responsible for the decrease of evolutionary rate.