The influence of ecological nitrogen limitation on the composition of plant genomes is still unclear. This study aimed to find the role of nitrogen source in the Sundarbans on the genomic nitrogen and base heterogeneity in the leaf and root DNA of two Avicennia species. DNA in mangrove leaf and roots were quantified by spectrophotometric method. The quantitative determination of individual bases in the DNA after acid-hydrolysis was accomplished by reverse phase high-pressure liquid chromatography with UV detection. DNA was digested with alkaline persulphate solution in an autoclave and P and N concentration in the digest were determined using spectrophotometric method. For total inorganic nitrogen, soil sample was extracted in 2 M potassium chloride solution and ammonia-nitrogen, nitrite and nitrate-nitrogen were determined in the extract by using spectrophotometric method. Inorganic nitrogen concentration in sediment was found low (4.04±1.06 μg g 1) and it exhibited positive linear relation with DNA nitrogen extracted from leaf (DNA-N = 0.005±0.0572 Sed-N, R 2 = 0.85) and root (DNA-N = -0.113±0.0791 Sed-N, R 2 = 0.9). N:P ratios in DNA were <4. In contrast to the roots (A-T 57.63-59.01%; G-C 40.89-42.34%), the percentage of G-G-base pairs in leaves (58.42-64.38%) was greater than the percentage of A-T-base pairs (35.58-41.57%). Low abundance of nitrogen in the soil results in the occurrence of N-poor nucleotides in root DNA. The mangroves seem to assimilate nitrogen from both soil and the atmosphere with atmospheric NOx uptake playing a greater role in leaf protein content than soil inorganic nitrogen. This study supports the hypothesis that higher levels of DNA with N-rich nucleotides in leaves relative to roots are necessary for enhance synthesis of protein to offset damage by photochemical processes. © 2011 Academic Journals Inc.