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The prevalence and genetic character of <i>Wolbachia</i> endosymbionts in field-collected <i>Aedes aegypti</i> mosquitoes were examined for the first time in Taiwan. A total of 665 <i>Ae. aegypti</i> were screened for <i>Wolbachia</i> infection using a PCR assay targeting the <i>Wolbachia</i> surface protein (<i>wsp</i>) gene. In general, the prevalence of <i>Wolbachia</i> infection was detected in 3.3% <i>Ae. aegypti</i> specimens (2.0% female and 5.2% male). Group-specific <i>Wolbachia</i> infection was detected with an infection rate of 1.8%, 0.8% and 0.8% in groups A, B and A&B, respectively. Genetic analysis demonstrated that all <i>Wolbachia</i> strains from Taiwan were phylogenetically affiliated with <i>Wolbachia</i> belonging to the supergroups A and B, with high sequence similarities of 99.4–100% and 99.2–100%, respectively. Phylogenetic relationships can be easily distinguished by maximum likelihood (ML) analysis and were congruent with the unweighted pair group with the arithmetic mean (UPGMA) method. The intra- and inter-group analysis of genetic distance (GD) values revealed a lower level within the Taiwan strains (GD < 0.006 for group A and GD < 0.008 for group B) and a higher level (GD > 0.498 for group A and GD > 0.286 for group B) as compared with other <i>Wolbachia</i> strains. Our results describe the first detection and molecular identification of <i>Wolbachia</i> endosymbiont in field-caught <i>Ae. aegypti</i> mosquitoes collected from Taiwan, and showed a low <i>Wolbachia</i> infection rate belonging to supergroups A and B in <i>Ae. aegypti</i> mosquitoes.