Half of the aquatic products directly used for human consumption in the world comes from Aquaculture. This industry is the fastest growing food producing sector globally. Given the global population is growing, and there is an increase in urbanisation and wealth, aquaculture is expected to expand to meet the food demand, and most of this growth will be through intensification of existing farming areas. As this growth occurs, infectious diseases have been a serious impediment. Infectious diseases have significantly plagued different aquaculture systems, including open mariculture farms where the prevention and control of the infectious agents are particularly challenging as the sites are interconnected via a shared water environment. The primary aim of this thesis was to describe disease issues facing East and Southeast Asian marine fish culture, assess the likelihood of different infectious routes for marine farms in the Hong Kong Special Administrative Region (SAR) of the People’s Republic of China (PR China), develop biosecurity recommendations at the farm and area levels for these farms, and assess the economic costs and benefits that implementation of these biosecurity measures would have on the local farms. The Hong Kong mariculture industry consists of mostly small traditional cage farms, and they have been affected by a wide range of endemic pathogens, such as sea lice, Cryptocaryon irritans, and Vibrio spp. Also, there were reports of infection with red seabream iridovirus as a listed pathogen by the World Organisation for Animal Health (WOAH), among others. Our evaluation of pathogen transmission pathways in Hong Kong mariculture farms revealed that the likelihood of pathogen introduction on farms was the highest for water routes and new fish stock. We also identified several issues for the spread of pathogens within farms, such as the lack or improper dead fish removal on farms and a delay in fish treatments. Accordingly, we developed biosecurity guidelines for Hong Kong marine fish farms taking all the identified pathogen transmission pathways into consideration. These guidelines targeted prevention and or control of infectious diseases in Hong Kong mariculture at both farm and area levels. We realised that given the current status of mariculture system in the region (i.e. small-scale traditional cage farming) and the demand for live fish markets, which has necessitated local farmers stocking their sites with multiple species on a frequent basis, it is difficult to implement some management strategies. Further, for some measures, for example water disinfection technology, vaccination, and using commercial feed, the implementation of these practices could be costly compared to their earnings. We developed a model to assess the economic performance of a typical marine fish farm in Hong Kong SAR and estimated the profitability of different biosecurity plans. Our results indicated that most biosecurity measures recommended for aquaculture are not cost effective for small-scale farms, such as the case in Hong Kong marine cage culture. However, adding a minimal level of biosecurity including early detection and treatment of diseased fish and prompt removal of dead and moribund fish was observed to be most profitable on these farms with low or medium levels of expected mortality. Our results also revealed that these measures may pay off when high mortalities occur on these farms. In addition, according to our model, increasing the number of fish stock on Hong Kong marine fish farms can compensate for the high expenses of biosecurity strategies. However, the risk associated with overloading fish farming areas that are already stocked at high density could be problematic. Overall, to ensure biosecurity in Hong Kong mariculture farms, the industry requires to be restructured. However, it should be noted that any changes in the current farming system need to align with the needs of farmers and their life styles as many of them have owned their licences for generations.