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 seven samples from Rock Garden Beach Resort, 5 hours west of the village and two DNA samples were extracted using the CTAB method, then the technique. Sequence-related Amplified Polymorphism (SRAP) to assist in detecting genetic variability of sea grass. The Phoenix Mercury in monitoring all 12 pairs found the DNA of 53 DNA appeared fragments are monomorphic bands of the 22 DNA, representing an average 1.83 fragments per pair primer and. DNA polymorphic bands 31 are used for an average of 2.58 per match DNA prime-Mercedes. 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.