Origin recognition complex 6 (Orc6) plays a central role in the initiation of DNA replication in all eukaryotic systems. The exact contribution of Orc6 to replication initiation has yet to be elucidated. Here, we analyzed the evolutionary dynamics of Orc6 in 15 vertebrates. Positive selection was detected in the region of exon 6 of the Orc6 gene. Site tests revealed a proportion of codon sites that displayed evidence of positive selection (ω > 1) within the coding sequences of the vertebrate Orc6 gene. Seven positively selected amino acid sites were identified and three were located in exon6. These results suggest that amino acid residues present in the middle region of the protein are more selectively constrained, whereas amino acid residues in the C-terminal peptide of the protein evolve at a faster rate, possibly because of heightened selective pressure during the course of evolution.