The Persian Gulf coral reefs continue to suffer from impacts of anthropogenic activities and climate change, losing much of its coral cover in the process. Understanding the extent of connectivity among populations within a certain area can assist in conservation efforts and the design of Marine Protected Areas. The goals of the present study are: (1) To quantify patterns of genetic variation across six reef patches in the northern Persian Gulf and Gulf of Oman; (2) To infer levels of gene flow among adjacent sites and among distinct reefs; (3) To determine the source populations of juvenile colonies of the three species with different mode of reproduction; (4) To investigate how these genetic patterns vary among species with different life histories; and (5) To simulate the drift and active swimming of coral larvae under the influence of forcing changing on daily to multi-annual time scales.