Microbial symbionts play important roles in insect biology, but their diversity, distribution, and dynamics over time across host populations are poorly understood. We surveyed the spatio-temporal distribution of bacterial symbionts in the broadly distributed and economically significant leafhopper genus Macrosteles, with emphasis on Macrosteles laevis, using host and symbiont marker gene amplicon sequencing. The cytochrome oxidase I (COI) gene data revealed no strong genetic differentiation across M. laevis populations, significant levels of heteroplasmy, and multiple cases of parasitoid infections. 16S rRNA data confirmed the universal presence of the ancient nutritional endosymbionts Sulcia and Nasuia and a high prevalence of Arsenophonus. Interestingly, in contrast to most previously surveyed species, in M. laevis we found only occasional cases of infection with facultative endosymbionts and other bacteria. There was no significant variation in symbiont prevalence across populations, or among sampling years for the same population. Facultative endosymbionts including Rickettsia, Wolbachia, Cardinium, and Lariskella, were more common in other Macrosteles species. Combined, our data demonstrate that not all species show clear spatial and temporal variation in genetic structure and microbial prevalence. However, simultaneous characterization of host and symbiont marker gene amplicons in large insect collections can help understand the dynamics of host-microbe interactions.