Seagrass is vital to the ecosystem. The sea grass is as a producer. It is a source of fish nursery and refuge. A study in the Indo-Pacific - the sea grass species Halodule pinifolia fall into a state threatened. Risk of extinction. So in this research study. The study focused on the genetic variability of sea grass species. The samples of seagrass H. pinifolia all 7 samples from Rock Garden Beach Resort 5 samples, chomtawan village 2 samples. Were DNA extracted using the CTAB method, then the technique. Sequence-related Amplified Polymorphism (SRAP) to assist in detecting genetic variability of seagrass. Using a primer in check all 12 pairs found the DNA of 53 DNA bar appeared fragments are monomorphic bands of the 22 DNA bar, representing an average 1.83 fragments DNA bands per primer pairs. DNA polymorphic bands 31 DNA bar are used for an average of 2.58 fragments DNA bands per primer pairs. By the genetic variation found that, on average, 58.49 percent of which can be said. The genetic variation that occurs. As a result of adaptation to the environment for the survival of sea grass.