The invention discloses an individual labeling method for selective breeding of tilapia. Firstly, an appropriate plastic pin, a tagging gun, a closed loop plastic tag and so on, are selected; secondly, Tricaine methane sulphonate with a concentration of 0.33g/L is used to anesthetize the tilapia; and then a fish body is labeled. The tilapia is kept a posture of swimming during the labeling and faces toward the left side; an insertion point is positioned at the front end on the back of the fish body; the closed loop plastic tag is sleeved on a gun needle; the plastic pin directly passes through the fish body to fix a label, and the length of the plastic pin exposed outside the fish body is between 2 and 4cm; and finally the labeled tilapia is placed into a 10 percent povidone iodine solution for soaking disinfection. The method has the advantages of simple operation, low cost, and high automation, has less damage degree to the fish body, ensures that the retention rate of the label is more than 90 percent and the effective recognition rate is more than 90 percent, can not affect the normal activity of the tilapia, and can meet the need of large-scale labeling of selective breeding of the tilapia.