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The Ogasawara Islands, representing an oceanic island ecosystem in Japan, have a notably high rate of endemic species akin to other oceanic islands globally. Pittosporum parvifolium is a critically endangered shrub with only four remaining individuals in its natural habitat on the Ogasawara Islands. Current conservation efforts encompass both in situ and ex situ approaches for P. parvifolium. However, these efforts face challenges stemming from the lack of critical conservation information. Therefore, we explored P. parvifolium's genetic diversity and implications for conservation. We utilized simple sequence repeat markers to scrutinize genetic diversity within both in situ and ex situ populations, revealing notably rich diversity among both. The in situ genetic diversity was significantly high despite the few extant individuals. In addition, many of the ex situ peculiar genotypes were absent in individuals conserved in situ. This investigation also provides insights into the reproductive strategies and combinations of selfing and outcrossing. The results of the present study recommend conservation to maximize genetic diversity in P. parvifolium by promoting cross‐pollination among in situ individuals and by introducing individuals with unique genotypes into ex situ stocks. [ABSTRACT FROM AUTHOR]