Pomegranate ( Punica granatum ) is an important horticultural and economical plant worldwide. Iran is one of the bestknow producers of pomegranate. In addition to its nutritional value for usual consumption, pomegranate also contains many compounds with anticancer, antioxidant and antimicrobial activities. Part of the biosynthesis pathways of these compounds are believed to be located inside the plastids and therefore, study of the chloroplast genes may help with better understanding of the production mechanisms of these compounds. rpl36 , rpoA and infA genes (encoding the ribosomal large subunit, RNA polymerase ? subunit and initiation factor I, respectively) are highly conserve among land plants. Taken in to consideration that there are no reports about these genes in pomegranate cpDNA, in the present study, they were studied and the information was used to analyze the phylogeny of the punica genus. Pomegranate cpDNA from leaves of cultivated, wild and ornamental pomegranates were extracted and genes of interest were isolated using PCR reactions and specific primers designed based on aligned cpDNA sequences from other plants. PCR products were sequenced and have been used to construct five nucleotide and three amino acid datasets. In summary it was found that sizes of the rpl36 and rpoA genes were 114 and 1014bp, encoding 37 and 337 amino acids, respectively. Pomegranate infA gene comprised of 240bp that included 8 stop codons. Hence infA may be in fact a pseudogene. On the other hand bioinformatics analysis of the sequence 5’ UTR pointed to the likely presence of promoters and therefore possible existence of a RNA editing process that modifies the gene internal stop codons to amino acid codons. Among cultivated, wild and ornamental pomegranates, infA gene was completely conserved while rpl36 and rpoA genes showed few differences in their sequences. Based on results of the total dataset, oenotera was the closest evolutionary lineage to punica . Eucaliptus from Myrtales order, has been also dir=rtl Key words: chloroplast genome, angiosperms phylogeny, Punica granatum , rpl36 , rpoA , infA , specific primer
