Among different ecosystems, mangroves are very exclusive that they are marginal ecosystems and distinctively well-defined by marked boundaries with high and low tide levels. A better understanding of the interaction between ichthyoplankton and its nursery ground is essential for protecting the threatened fish stocks and this information could provide insights on the impact of coastal degradation on fish nursery ground. However, identification of fish eggs up to species level is very difficult due to the lack of distinguishing visible characters. The cytochrome c oxidase subunit 1 (COI), a mitochondrial gene has been standardized to discriminate all the animal species. Further, ichthyoplankton diversity in mangroves can be a useful indicator of the state and health of an aquatic ecosystem. Ichthyoplankton samples can reflect their spawning output and provide an index of relative population size for the fish. Variation in the size of fish stocks can be detected more rapidly and sensitively by monitoring the ichthyoplankton associated with them. Despite the importance of mangroves as anursery area for aquatic fauna, research on the early stages of aquatic fauna, their biology and ecology in the mangrove ecosystem have not been studied so far.