In the culture of mud crab Scylla serrata, cannibalism is often the greatest cause of mortality. A laboratory study was conducted to compare the influence of size class differences and shelter on cannibalism and limb loss in juvenile mud crabs (20-70 mm internal carapace width; ICW). Four size classes of juvenile crab (A: 21-30 mm, B: 31-40 mm, C: 41-50 mm and D: 51-70 mm ICW) were tested in all possible combinations using four different substrata with varying degree of shelter (seaweed, plastic strings, bamboo tubes and open sand substratum) in 48 h trials. Results suggest that cannibalistic interactions are heavily influenced both by size differences of crabs and the availability of shelter. Cannibalism on the smallest size class (20-30 mm ICW) increased about 10 times in the presence of the largest crab (51-70 mm ICW) compared with treatment with only same-size crabs (control treatment). Shelter provided little refuge for the smallest crabs, whereas cannibalism in larger size classes decreased by >50% in all the shelters compared with the sand substratum. The findings suggest that both size-grading and provision of shelter could minimise cannibalism in the culture of mud crabs.