Pomegranate is an economically important genus that includes valuable biochemical compounds where synthetized in chloroplast organel. Therefore understanding the characterestics of plastid genes by molecular sequence analysis authorized us to elucidate mechanism of their production. The chloroplast genome is 160,129 base pair in length and includes a pair of inverted repeats (IR) of 26,996 base pair separated by small and large single copy (SSC, LSC) regions of 18,393 base pair and 87,744 base pair, resepectively. The l and f contribute in photosynthesis, especially for functional process of photosystem II. These genes were aligned with their counterparts in 23 different plants which were exist NCBI gene bank. According to this comparison, PCR primers were selected using the primer selection computer program oligo 5. Finally the genes were amplified with selective primer pairs and were sequenced. On the basis of the results, the aligned part of l and f genes had a length of 117 and 120 bases respectively, which encode two significant proteins comprising 38 and 39 amino acid residues. l and f genes had a ACG and ATG as a first codon respectively. The alignment of the l and f nucleotide sequences from 26 plants shows strong conservation. According to the results and analyzing the sequencing patterns of 3 groups of pomogarante genus which encompasses wild, ornamental and domesticated ones, with MEGA 4 software, the relationship among 26 genotypes represented by the Minimum-Evolution dendrogram. In the phylogenetic tree, wild, ornamental and domesticated genotypes of pomegranate genus completely separated and Key words: punica granatum , l gene, f gene, photosystem II, genom chloroplast.
