The abundance of epiphytic algae on seagrasses, the result of interactions among many biotic and/or abiotic factors, can largely determine the impact intensity and the direction of the pros and cons. This paper systematically reviews the information on the effect factors on the abundance of epiphytic algae in the past two decades, the results show three main regulatory factors: physiological characteristics of seagrasses, biological factors (grazing by herbivores), chemical factors (nutrients concentration), and physical factors (irradiance and water motion). Among them, grazing (the main form of top-down) and nutrient concentration (the main form of bottom-up) are relatively important. Finally, the important aspects for the further study are pointed out: ① Relative roles of top-down and bottom-up factors in seagrass ecosystem and their quantification; ② Reaction of epiphytic algae to separate and combined factors; ③ Mechanism of the chemical defenses released by seagrass to regulate the epiphytic algae; and ④ the influence mechanism of epiphytic algae on seagrass.