Genetic variation of seagrass species H. uninervis and H. pinifolia with varying leaf width, from different sites, density and exposure in the Central Visayas were assessed using plastid rbc L marker specific for Halodule . The genetic structures of the rbc L sequences analyzed from 83 specimens of Halodule uninervis and H.pinifolia were 671 base-pairs (bp) long (with a difference of 2 base pairs (bp) substitutes of A in uninervis to C and G in pinifolia ). All specimens of Halodule from three different sites in Central Visayas were clustered only into clades: H. pinifolia and H. uninervis , maintaining that despite significant morphological variation in leaf width due to different sites, density and exposure, the two are still separate species. Keywords - seagrass, DNA, rbc L marker