Cyanobacteria are often used as an indicator of the presence and level of pollutants in the environment. They have been especially recognized for their ability to identify contamination of heavy metals. Class II metallothioneins (MTs). usually found in cyanobacieria, are low molecular weight metal-binding proteins and may be required for heavy metal tolerance. It will be important to examine the phylogenetic pattern as well as prokaryotic evolution of metal-binding protein families among cyanobactena. All the available protein sequences of cyanobacteria metallothioneins from GenBank, PDB and Pfam have been aligned and the phylogenetic tree was constructed by utilizing four multiple sequence alignment software ClustalW, T-Coffee, POA and GCG-PileUp. Eight cyanobacteria included in this study were Synechococcus sp. PCC 7942, Synechococcus sp. WH 8102, Thermosynechococcus vulcanus, Thermosynechococcus elongates BP-1, Nostoc sp. PCC 7120, Gloeohacter violaceus PCC 7421, Oscillatoria brevis, and Magnetospirillum magnetotacticum. 22 reported heavy metal resistant sequences from these 8 species of cyanobacteria were aligned. A phyletic pattern search tool provided by Cluster of Orthologous Groups (COGs) database, a collection of COGs from 63 sequenced prokaryotes and 3 unicellular eukaryotic genomes was also used to select a desired pattern of presence-absence of species . Cn3D 4.1 program was used for structural alignment. The results indicated that the tree was composed by five clusters. Most Synechococcus and Thermosynechococcus were clustered into 2 clades while others had relatively far genetic distance with Synechococcus but closely linked to each other. Structure alignment of metallothionein among cyanobacteria indicated that a major portion of their structure are not identical but with similar properties such as polarity. The results clearly showed several conserved C-X-C motifs near N-and C-terminus of Class II metallothioneins.