Aquaculture is an upcoming industry in Malaysia as sustainable fish production with total production of 407,387 tonnes in 2016. As a growing industry, current practices have led to disease outbreaks which are highlighted as one of the major issues faced in aquaculture farms. Throughout the 20 years of disease reporting in Malaysia, several bacterial and viral diseases were found to persist in farms. In addition, emerging global diseases have also been detected in several farms. The consequence of these diseases were outbreaks led to huge economic losses. Eventually, the combination of persistent and emerging diseases creates a potential threat for the aquaculture industry and hence requires immediate attention. Therefore, this review summarises the major viral and bacterial pathogens of fish and crustaceans in the context of Malaysian aquaculture. It also considers the characteristics of disease and their impacts as well as the potential for future disease emergence in these aquatic animals as aquaculture industry continues to expand. This review serves as a platform for future directions in research in improved monitoring, detection and prevention as a step towards increasing biosecurity in Malaysian aquaculture.