The distribution of lobsters in Indonesian waters is very wide, even lobster species in Indonesia are also scattered in the tropical waters of the western Pacific Ocean, the Indian Ocean, Africa to Japanese waters. Indonesian waters are divided into 11 (eleven) Fishery Management Zone (FMZ). Lobsters in Indonesia may come from various water areas, both national and regional water zones, and they’re called the sink population. Its spread is influenced by the movement of the current. Lobster seed is nurtured by nature through ocean currents from Australia, East Indonesia, Japan, then back to Australia. Lobsters have a complex life cycle, where adult lobsters inhabit coral reefs as a place to lay eggs, then hatch into planktonic larvae, and grow up in open seas and carry out diurnal and ontogenetic vertical migrations before returning to nurseries in shallow coastal areas and reefs, coral, as well as habitat by the type of species. Literature research had used at least two methodologies to estimate the distribution and connection sensitivity matrices of marine organism larvae. The two most common approaches are using genetic markers and numerical biophysical modeling. Thus, this research uses molecular genetic techniques to explain the genetic structure of lobster populations using a biophysical model approach that can explain the genetic structure of lobsters, as well as the distribution based on regional oceanographic synthesis data and lobster biology known in Indonesian waters. This model has four components, namely: 1) a benthic module based on a Geographical Information System (GIS) which is a lobster habitat in the spawning and recruitment process, 2) a physical oceanography module containing daily velocity in the form of a three-dimensional hydrodynamic model, 3) a larva biology module that describes larval life history characteristics, and 4) a Lagrangian Stochastic module that tracks the individual trajectories of larvae.