Members of the brackish-water species Lamprothamnium succinctum (Charales, Charophyceae) are widely distributed from tropical to temperate regions, including East Asia. In Japan, L. succinctum is listed as an endangered species and is protected by the government, because it was recorded only at two localities, Lake Hachiro-gata (Akita Prefecture) and Oo-ike pond (Deba-jima Island, Tokushima prefecture), and has become extinct in the former. In this study, we identified five new localities of this species in Japan. The morphological characteristics of their thalli agreed with those provided in the original description of this species, with distinctive reproductive characteristics. Moreover, the oospores of Japanese specimens of L. succinctum were examined for the first time using scanning electron microscopy. The oospores of Japanese specimens exhibited granulate fossa wall patterns, which were consistent with those described in previous studies. Our genetic analyses based on the DNA sequences of two chloroplast DNA markers, including both the coding and non-coding regions, revealed that the sample from Oo-ike pond is distinguishable from those from other Japanese specimens, although they are genetically very similar.