Freshwater jellyfish comprising the genus Craspedacusta are thought to have originated in the Yangtze River, China and have since spread to all continents except Antarctica. In this study, jellyfish were collected from Haruta-ike, an artificial pond in Chikuma City, Nagano (Japan). Medusae were identified as Craspedacusta sowerbii using morphological and molecular techniques. Despite the existence of Haruta-ike since prior to the Edo era (ca. 1603), this work represents the first published record of freshwater jellyfish in this pond. Herein, we report on the novel swimming behavior documented in this population, which includes both male and female C. sowerbii medusae. Additionally, we discuss the life cycle of polyps reared in culture from Machikane-ike, a pond in Osaka for which we have published the first complete mitochondrial genome of C. sowerbii from Japan. Finally, we report on the morphology and life cycle of the rare Japanese freshwater jellyfish Astrohydra japonica in Lake Biwa (Shiga), documented only a few times in the 40 years since its original discovery in Japan. The results of our robust phylogenetic analysis using the 16S rRNA gene and COI markers of C. sowerbii and A. japonica in this study and for C. sowerbii material from Singapore, together with all publicly available sequences for these markers for the two species worldwide, revealed two major C. sowerbii clades suggesting the Nagano and Osaka populations originated from two distinct introduction events. This collaborative research was made possible through international collaborations among multiple research facilities, museums and one wildlife reserve.