This study has observed an overall high genetic diversity within populations of horseshoe crab T. gigas and has a low lavel of genetic differentiation which indicates a population connectivity and a single stock population. With regard to the limited movement potential of coastal horseshoe crabs, it should be noted that historical demography was part of the population expansion during the last glacial period. Therefore, local-based conservation is the preferred management method, which can be one of the precautionary approaches to conserving the Indonesian coastal horseshoe crab. Additionally, an advanced analysis based 19 on male and female horseshoe crab needs to be elucidated with characteristic of population subdivision from the nuclear genome (e.g., microsatellites) and requires the expansion of the number in geographic range around Indonesia.