There are ecosystems even in the center of huge urban areas. To understand the environmental factors affecting urban biodiversity could make urban ecosystems more functional for human life and other “natural” ecosystems. Urban greeneries are generally the most abundance of biodiversity in urban area and fragmented as well. However, how and what degree of the fragmentation affect animal populations among urban greeneries have been unclear with some exceptions. The common methods to estimate or trace the migration of animals, such as using mark-recapture and telemetry, should be useful in urban area, but have some disadvantages. Here, we estimated the degree of migration among butterfly populations in urban greeneries from genetic variations using DNA markers. The pale grass blue, Zizeeria maha, was collected in urban greeneries of central Tokyo, that is a historical city where the greeneries are remarkably fragmented. We newly developed polymorphic compound microsatellite markers using an adaptor-ligated library method targeting to the compound single sequence repeats (Lian et al. 2006). The development of microsatellite DNA markers for use with Lepidoptera has described “extremely difficult” (Zhan 2004), but this study presented a valid method. The genetic variation among populations of the pale grass blue in central Tokyo was discussed.