Intra- and inter-specific competition for shelter, in relation to prior residence, sex differences, and body-size effects, was studied in the laboratory to assess the potential impact of the alien crayfish species Pacifastacus leniusculus on the endangered Japanese endemic crayfish species Cambaroides japonicus. The resident was placed in an aquarium, which contained a single shelter of preferred size for both C. japonicus and P. leniusculus. After 24 h, the intruder was introduced into the aquarium. In the experiments using different sex pairs of crayfish of approximately equal size, male residents had a significant prior residence effect against female intruders in both crayfish species in the intraspecific contests. However, residents of P. leniusculus dominated C. japonicus regardless of the sex in interspecific contests. In experiments using male crayfish pairs of different sizes, larger individuals had more successful possessions of the shelter against smaller individuals regardless of crayfish species. The body-size advantage strongly influenced the outcome of the both intra- and inter-specific contests regardless of residents or intruders and overcame the prior residence effect in both species. These results suggest that P. leniusculus is superior to C. japonicus in shelter competition if P. leniusculus invades the habitat of C. japonicus.