In order to study the effects that climate change and pollution have on the environment long term monitoring of the environment is necessary. One of the most important natural environment so never thought of the coral reefs, however, monitoring the fish population and biodiversity is still a challenging task data collection in this kind of environment is labor-intensive requiring divers to count the fish species in a certain area in recent years. Digital video recording has become much cheaper which makes underwater cameras a good alternative for data collection. Furthermore, automatic video processing and pattern recognition are able to process this kind of data, this paper describes an entire system which is being developed to allow marine biologists to analyze large amounts of video data for long term monitoring purposes. To give an indication of the challenges in this project summary is given of the amount of data that the system is expected to process at the moment.