Comparing and aligning multiple genomes can produce valuable information regarding the species revolution. EMAGEN is an efficient algorithm to compare and align closely related multiple whole genomes. It aligns multiple whole genomes by first finding globally optimal consistent conserved regions among multiple genomes, then generating detailed alignment of the gaps between consecutive conserved regions with Clustal W. It uses two methods to find the globally optimal consistent conserved regions: Direct Matching and Functional Matching. DM method is to align genomes directly with their DNA sequences. FM method is used especially to align multiple prokaryotic genomes with their concatenated protein sequences. In this paper, We apply both methods of EMAGEN to prokaryotic genomes. Various experiments are performed with EMAGEN and their results are displayed and discussed. The results show that EMAGEN performs very well in the experiments and is very useful to compare different prokaryotic genomes.