Gut microbiota have been reported to be closely linked with development of the intestinal tract, nutrition, immune response, and disease resistance by the host animal. However, most previous studies have focused on the underlying factors that determining the differences in gut eukaryotic communities between lean and obese animals and human, there is little knowledge about Community structure difference of gut eukaryotic microbiota among cohabitating retarded, overgrown and normal shrimp. This is the first attempt on a study that aims at jointly defining the phylogenetic clustering and interspecies interaction of the gut microbiota among shrimp categories.