Structural heterogeneity results in different spatial distributions of microcrustaceans. Thus, in ecosystems with excessive macrophyte development, it may be difficult to determine the microcrustacean species composition. Given the importance of microcrustaceans in the food web, the elucidation of microcrustacean diversity is essential. In vegetated habitats, bluegill sunfish can prey on microcrustaceans, and therefore have a potential role as microcrustacean monitoring agents. In the present study, we compared microcrustacean species compositions in the field with those in the guts of bluegill, in Jangcheok Lake, South Korea. Our results showed that the number of microcrustacean species was higher in bluegill guts than in the field. Further, microcrustacean species, such as Daphnia galeata, Graptoleveris testudinaria, Leydigia leydigii, Rhynchotalona sp., and Simocephalus exponisus, were found only in bluegill guts. Our findings verify the validity of the fish gut analysis to monitor microcrustacean species compositions and to clarify spatial distributions of microcrustacean species in structurally heterogeneous ecosystems with excessive macrophyte development.