Abstract—Endosymbiotic relationship between Wolbachia (Rickettsiales: Rickettsiaceace) and braconids species is a new topic to be discussed among researchers due to its potential as biocontrol agents of fruit flies species. In this study, Wolbachia Surface Protien (wsp) marker has been used to detect the existence of Wolbachia molecularly that associated with braconids (Opiinae) collected from several localities throughout Peninsular Malaysia Our results revealed that five species of parasitoids viz. Fopius arisanus, F. vandensboschi, Psyttalia sp., P. fletcheri and P. incisi were symbiont positively with nine different strains of Wolbachia. A total of nine strains have been successfully sequenced and classified into three Wolbachia subgroups namely Mel, Ri, and Inc based on the results of clustering analysis. In this study, Inc Wolbachia group has been known as a novel group emerged of Wolbachia. These data should be useful in future Wolbachia-based biological control program that involving parasitoids and fruit flies.