The endosymbiont Wolbachia, extensively occurring in arthropods, usually causes reproductive distortions of the host, such as mosquitoes. In past years, detection of Wolbachia in host tissues has highly relied on transmission electron microscopy (TEM) that is tedious and usually unable to gain satisfactory results without experienced techniques and expensive instruments. Polymerase chain reaction (PCR) recently has become popular in Wolbachia identification. However, necessity of DNA extraction from host individuals or dissected tissues has limited its application in extensiveness and versatility. At present, in situ hybridization has increased its role in examination of various microbes. This report provides a technique for rapid detection and localization of Wolbachia in tissues dissected from mosquitoes and possibly other infected organisms. To detect Wolbachia and to localize them in host tissues more precisely, in situ hybridization by using digoxigenin (DIG)-labeled probes was invented and applied to Wolbachia detection in this study. The results showed that Wolbachia preferentially aggregate in ovarioles, which is consistent with previous observations by TEM. The endobacteria also were detected in salivary glands, mostly in lateral lobes. Ultrastructurally, Wolbachia has been shown to occur in the cytoplasma of salivary gland cells.