Molecular identification data of unexplored Indian Rhizophoraceae an eco-friendly mangroves are an imperative aspect in molecular phylogenetics. We describe the phylogenetic relationships among the Rhizophoraceae genus Rhizophora, Ceriops and Bruguiera using tRNA Leu (UAA) intron sequences as a molecular marker. The results of present study reveals congeneric relationship between R. apiculata, R. mucronata, B. gymnorhiza indicating a high degree of gene flow within them and the pairwise distribution of study plants among Rhizophoraceae family. The phylogram constructed using tRNA Leu sequence clearly clustered the species of the same genus in individual group. The stem-loop could be divided into two classes, both built up from two base pairing heptanucleotide repeats. Size variation was primarily caused by different numbers of repeats but some strains also contained additional sequences in this stem-loop. The statistical summaries of DNA sequence data can enable to identify the structural signature of the genome as well as to classify phylogenetic relationships among different species reflected in the difference of genetic diversity distributions within their DNA sequences.