Nardonella (gamma-proteobacteria) are a group of ancient endosymbiotic bacteria that occur only in weevils (superfamily Curculionoidea). Despite the extensive surveys of their existence and phylogeny done in a number of weevil subfamilies, little is known about their strain diversity, quantitative dynamics, and biological roles in the ontogeny of hosts. Here, based on the cloning and analyses of bacterial 16S RNA gene sequences from nine geographic populations of rice water weevil, Lissorhoptrus oryzophilus Kuschel (Coleoptera: Curculionidae), we identified two distinct Nardonella lineages. One lineage was widespread, occurring in each of the L. oryzophilus populations investigated, whereas the other was much geographically limited and found in only one population. These bacteria had a low density in both larval and pupal stages of the weevil; however, they increased substantially as adults emerged. In female adults, they were harbored dominantly in ovary; guts were also infected, but the density was very low. By treating adult females with various antibiotics (rifampicin, tetracycline, and gentamycin) and observing their fecundity, egg viability, as well as the density of Nardonella and the other two bacteria (Wolbachia and Rickettsia) present in the ovary, we found females did not produce viable eggs despite the presence of abundant Nardonella. This suggests that Nardonella might be not playing critical roles in the reproduction of L. oryzophilus. The results are expected to extend our knowledge of the biology of Nardonella and their associations with weevils' reproduction.