In the present study, it was observed how the phage-host system that is naturally reproduced in activated sludge is affected by the host inoculation. The system of Microlunatus phosphovorus and its phages was selected as the phage-host system native to an activated sludge system operated for 19 days under sequencing anaerobic-aerobic conditions with glutamate as the main carbon source. The phage-host system related to M. phosphovorus was monitored by plaque assay for the phages and by fluorescent in situ hybridization (FISH) for the bacterial host. In addition, the whole phage structure was also monitored by pulsed-field gel electrophoresis (PFGE). During the first 9 days, the phage-host system was more or less steady at approx. 9% (FISH/ DAPI) for M. phosphovorus and approx. 10,000 PFU/ml for its lytic phages. Microlunatus phosphovorus JCM9379 was inoculated into the activated sludge on day 10. Right after the inoculation, M. phosphovorus was approx. 24% (FISH/DAPI) whereas its lytic phages dropped down to approx. 500 PFU/ ml. After the host inoculation (within 9 days), however, the phage-host system eventually reverted to its original level in each population. On the other hand, the whole phage structure was not significantly changed by M. phosphovorus inoculation but stable throughout the process operation. Only the minor change that four phage groups gradually became abundant after the host inoculation was observed.