Searching for unique features of archaeal genome may shed light on the mechanism of gene regulation in primitive life forms. Statistical analysis of ATG frequency on the complete genome sequences of 16 archaea, 20 bacteria and 2 eukaryotes revealed that most of the archaeal genomes have a remarkably high ATG frequency at the position of nine nucleotide (nt) downstream of the translation initiation site (the first nucleotide of the translation initiation codon is designated as 0). To understand the role of this unique ATG in archaea, we further analyzed the ATG-initiated genes and non-ATG-initiated genes separately, and the results indicated that only the non-ATG-initiated genes contribute to the high ATG frequency at position +9. This led us to speculate that the in-frame ATG at +9 may serve as a remedial initiation site for archaea in case of initiation failure at the regular site. In addition, it seems that this phenomenon does not result from the harsh environment that archaea are usually viable according to the fact that no considerably high ATG frequency at +9 was observed in all the four thermophilic bacteria that also live in harsh environment. We proposed that the high ATG frequency at position +9 might reflect the decreased efficiency of the translation initiation machinery in archaea. Since archaea evolve very slowly, this unique characteristic of high ATG frequency at position +9 may present the primitive state of the Universal Ancestor.