Given the economic and ecological values of coastal ecosystems in South East Asia, their preservation represent a tremendous environmental stake. Estuaries, mangroves and coral reefs, for example, provide resources and income for millions of inhabitants in these regions. However these ecosystems are severely threatened by anthropogenic and climatic pressure, which are often closely related. Recent findings have revealed that microbes and their viral parasites are highly abundant and dynamics in coastal waters. We also now know that they can quickly respond to environmental perturbations, and therefore represent excellent indicator of ecosystem health status. Here, we take the emblematic example of coral reefs in which the specific interactions between bacteria and viruses are now strongly suspected, according to the environmental conditions (water quality, temperature, salinity, contaminants, etc.), either to reinforce coral stability or conversely fasten their decline. Ongoing projects conducted in Vietnam aim at further investigating such poorly known mechanisms, which could promote the development of pioneer works for a better protection of marine resources.