We have analyzed the DNA sequences of the mitochondrial cytochrome oxidase subunit l(COX)gene in algae, We found the deduced deviant genetic codes where UAG codes for alanine or leucin e in Chlorophyceae, UGA codes for tryptophan in Prymnesiophyceae and AUAcodes for methionine in Xanthophyceae. Examination of the mitochondrial genetic codes in algae appears to be a very useful genetic marker for classification of algae when it is considered with the results obtained through a molecular phylogenetic tree. By using both approaches with a molecular maker and a morphological maker, the relationship among algal species will be confirmed.