<p>Pronodularia japanensis is a freshwater mussel (family Unionidae) endemic to Honshu, Shikoku and Kyushu in Japan. This unionid species prefers running water, and its main habitat is currently agricultural ditches. In this study, we report a newly found population of this species in an agricultural ditch in the alluvial Dozen Plain, in Ehime Prefecture, Japan. In Ehime, P. japanensis was previously recorded as inhabiting only the Matsuyama Plain and Uwa Basin, and its distribution area and density have been rapidly decreasing for decades; hence, this species is protected as endangered in Ehime Prefecture. We conducted a survey of an agricultural ditch in the Dozen Plain that was scheduled for rerouting during farmland consolidation. We found 651 P. japanensis individuals, with a maximum density of 20 individuals/m2, in an earthen ditch with a width of approximately 1 m and a length of 440 m. In total, 1,249 individuals were estimated to inhabit this earthen ditch. In a 60-m section where both revetments were covered with concrete, the density of P. japanensis was quite low. The mean shell length of P. japanensis was 41.7 ± 5.8 mm, and the standard deviation was larger than that of the Kunichi River population on the Matsuyama Plain. Therefore, the life span of the mussel in this earthen ditch is estimated to be shorter on average than in the Kunichi River, and reproduction occurs repeatedly. In the study area, although agricultural ditches for rice paddies form a network of aquatic habitats on the alluvial plain, most are concrete-covered due to previous farmland consolidation. Therefore, the earthen ditch examined here is one of the very few remaining in this area, and likely represents part of the last remaining habitat of unionid species. Pronodularia japanensis is listed as a near-threatened species in Japan, and conservation of the study population is necessary. Freshwater mussels are under threat of further decline due to anthropogenic influences; conservation of this species while also maintaining the adjacent agricultural field could serve as a good example for other areas.</p>