WO is a temperate bacteriophage that infects Wolbachia, a maternally inherited endosymbiont of arthropods. WO has lysogenic and lytic cycles, the latter of which is an important process for the spread of WO infection. In this study, we measured the lytic activities of two WO phages, WOCauB2 and WOCauB3, infecting a Wolbachia strain, wCauB. In the lytic cycle of WO, both ends of the prophage are ligated to create a junction sequence called attP in the phage genome. We performed real-time quantitative polymerase chain reaction to measure the amounts of attP sequences produced by WOCauB2 and WOCauB3 in wCauB-infected Ephestia kuehniella (Zeller) (Lepidoptera: Pyralidae) and wCauB-infected insect cell lines. WOCauB2 produced the phage genome more actively than WOCauB3 in E. kuehniella, whereas WOcauB3 was more active than WOCauB2 in the cell lines, suggesting that the environment of host cells in which Wolbachia is harbored affects the lytic activity of WO phages. The lytic activity was constantly very low: the amounts of attP relative to the prophages were lower than 1 × 10−3 in all measurements, which was discussed in conjunction with the intracellular life of Wolbachia.