The cultured cell‐based in vitro assay using the stringency of ligand‐receptor interactions is typically useful for screening certain hormone agonists from among a very large number of molecules. However, ligands are frequently altered or modified through evolution; indeed, even in the same receptor orthologs, different ligand sensitivity profiles are considered to arise among species and/or taxa. Such ligand transition has been observed in juvenile hormone (JH), one of the most important endocrine factors in arthropods. To understand the molecular basis of ligand selectivity alteration in hormone receptors, we compared the amino acid sequences and ligand selectivity of the JH receptor, Methoprene‐tolerant (Met), among three insects (Drosophila melanogaster, Aedes aegypti and Tribolium castaneum) and one crustacean (Daphnia pulex). Compared with D. pulex, we found that the receptors of the three insects showed a higher sensitivity to JH III, which is the major innate JH ligand in insects. Furthermore, point mutation analysis in Met sequences revealed a candidate amino acid residue that is important for increasing JH sensitivity in insects. Amino acid mutations in Met may have affected changes in ligand selectivity intermittently over the course of the evolution of the JH‐signaling pathway. These findings are useful to improve the existing (developing) cultured cell‐based assay system and may shed light on the relationship between functional diversification in hormonal signaling and the molecular evolution of hormone receptors. Copyright © 2017 John Wiley & Sons, Ltd.