Arafura Sea is well-known as the important area for commercial shrimp fisheries in Indonesia. The density of shrimps was highly influenced by their fishing pressure and environmental condition. The objective of this research was to study the distribution of shrimps based on its stock density and their relationship with the environmental variables. Trawling swept area method was used in 16 sampling sites of Arafura Sea during the transition monsoon in 2016. Some environmental variables in bottom layers as shrimp habitat were measured, including chlorophyll-a, dissolved oxygen, depth, salinity, temperature and pH. The results showed that the largest density of shrimps was found in the southern coast of Aru where it has the largest concentration of chlorophyll-a and dissolved oxygen. Among all the environmental variables, Chlorophyll-a was the main variable affected the density of shrimps. Three most dominant species were Penaeus semisulcatus, Metapenaeus endeavouri and Metapenaeus ensis. There was indication of the decreasing shrimp stock in Arafura Sea. The ecosystem-based fisheries management should be developed to rebuild the stock density and to enhance the environmental quality of Arafura Sea.