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In this study, we hypothesized that the limited geographical distribution of <i>Pseudopungtungia tenuicorpa</i> in South Korea is closely related to the local abundance of their preferred spawning habitats. Eggs of <i>P. tenuicorpa</i> were most frequently observed in cracks smaller than 5 cm, followed by the nests of other fish, such as <i>Coreoperca herzi</i>. Although eggs of <i>P. tenuicorpa</i> were also found in cracks larger than 6 cm, most of them were consumed or damaged by other fish. However, the number of <i>P. tenuicorpa</i> eggs spawned in cracks smaller than 5 cm remained similar to the number of eggs at the time of initial spawning, even after 9 days. The strong preference of <i>P. tenuicorpa</i> for cracks smaller than 5 cm was found to influence the geographical distribution of <i>P. tenuicorpa</i> in South Korea. In the upper reaches of the Han River, the ratio of cracks smaller than 5 cm is higher than that in the Geum River and in the Nakdong River, which contributes to the stable population growth of <i>P. tenuicorpa</i> there. In the future, management strategies to maintain/restore cracks smaller than 5 cm should be reviewed for the preservation of this endemic fish in South Korea.