CpG islands (CGIs) are often considered as gene markers, but the number of CGIs varies among vertebrate genomes that have similar numbers of genes. In this study, we first investigated the CGI distribution and density in nine vertebrate genomes. Second, we examined the distribution of CGIs in the promoter regions of human-mouse orthologous gene pairs and found many losses of CGIs in both genomes but the loss rate in the mouse lineage is two to four times the rate in the human lineage. Finally, we investigated the unique features of CGIs in the dog genome.