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The present study documented the presence of seagrass Halodule uninervis for the first time along with previously documented Halophila ovalis at Haripur creek. The population structure of both these seagrass species is assessed. The physico-chemical parameters were similar for both seagrass species except for the sediment grain size fractions. The sand content of H. ovalis patches was 1.2-fold higher than H. uninervis beds, whereas the silt content of H. uninervis beds was 2-fold higher than H. ovalis patches. The pH levels were lower than the standard oceanic pH of 8.2. Macroalgae like Ceramium sp. and Gracilaria verrucosa were growing on the leaves of H. uninervis due to high nitrate and phosphate levels of the creek waters. Leaf reddening was only observed in the leaves of H. ovalis. Under similar environmental conditions, H. ovalis (5004 ± 114.51 ind. m-2) had a 2-fold lower shoot density than that of the H. uninervis (11598 ± 187.52 ind. m-2). Both above- and below-ground biomass of H. ovalis (96.34 ± 10.18 and 197.5 ± 18.30 g DW m-2) was 2-fold lower than that of H. uninervis (198 ±7.45 and 456 ± 9.59 g DW m-2). H. uninervis leaves were 9-fold longer than that of H. ovalis, whereas H. ovalis leaves were 5-fold wider than H. uninervis. The leaf plastochrone interval is 2.3 days for H. ovalis and 9.6 days for H. uninervis. Consequently, the leaf growth rate of H. ovalis is 2-fold lower than that of H. uninervis. H. ovalis had 2.6-fold longer internodes than H. uninervis. The root length of H. uninervis was longer than H. ovalis. Consequently, the shorter root length of H. ovalis led to higher branching frequency than H. uninervis. The total C and N content were higher in the leaves of H. ovalis than H. uninervis.