Due to the trend of global warming, we should provide the new aquaculture policy to avoid damage from climate change. The aim of the project is breeding the temperature stress tolerance strain for Taiwan’s aquaculture and study in the effect of biological control of broneo mullet, which will instead of milkfish, for eliminating algae on clam pond. Molecular breeding, is more accepted methods for the selection of excellent species of fish in advanced countries. For improving the genetic traits stability of resistance to low temperature in breeding, we are establishing a systematic pedigree for species and genetic management of species in fish. The ways will avoid inbreeding degradation occurs, and establish fast-growing tilapia strains for selective group. In our tests of high temperature and low temperature process for screening associational molecular markers will be establish founder brooder group having rapid growth, resistant temperature stress performance. Research on the effect of biological control of broneo mullet for macroalgae on clam pond. In the pond stocked milkfish as the control group, the other 3 stocking density of broneo mullet as the treatments. the sample during the test once a month, measure body length, body weight and the rate of survival of the fish and clams. Every two weeks to analyze water quality and quantity of macroalgae species observed at the pond.