Wolbachia is a maternally-inherited, gram-negative symbiotic bacterium of arthropods, which causes a variety of reproductive alterations including cytoplasmic incompatibility (CI). CI occurs due to karyogamy failure and embryo death resulting when a Wolbachia-infected male mates with an uninfected female. A recently developed technique for maintaining Wolbachia in cell culture provides a simplified venue for characterizing the interaction between Wolbachia and host cells. A Fluorescence In Situ Hybridization (FISH) technique has been previously developed to visualize Wolbachia in early embryos. Here we will describe the modification of the embryonic FISH technique to allow the first detailed characterization of Wolbachia in a cell culture of Aedes albopictus (Asian tiger mosquito) cells. We will discuss how this technique can be used to answer fundamental questions including Wolbachia density in the different cell types that make up this heterogeneous cell culture.