Chironomus is a large genus of Diptera comprising about 400 species and occurs worldwide except for Antarctica. The strong morphological cross-taxon similarity of chironomid larvae renders identification at the species level difficult. Here, we analyzed the morphology of larvae of Chironomus flaviplumus, an easily cultured species employed as a bioindicator in polluted environments, to determine identifying morphological characteristics at the first through fourth instar. Observed differences appearing at each instar include the presence or absence of setae on the body and tubules on the 10th and 11th body segment, the number of seta interna in the mandible, and the presence or absence of ring organs in the antennae. Some specific morphological characteristics did not change after hatching. Our findings provide a reliable method for identifying C. flaviplumus larvae.