Abstract: Cotton biotechnology is achived mainly in genetic engineering.Cotton genetic engineering is succeeded due to progresses of Agrobaterium tumeficiens mediated method,particle bombardment method and pollen-tube pathway.Many transgenic cotton lines,which are acquired different forein genes including pest resistant gene,herbicide resistant gene,are applied in cotton breeding, subsequently,new varieties are commercialized in market.In china,it is advanced on transgenic bollworm resistant cotton in the world.Based on the research in our laboratory,this article indicates the applications and progress of biotechnology on the cotton breeding,analyzes the main problems in cotton biotechnology,and advises its developing strategy and suggestions.