<p>Gogi charr, <i>Salvelinus leucomaenis imbrius</i>, an endemic subspecies to the Chugoku Mountains in southwestern Japan, is one of the southernmost populations of the genus <i>Salvelinus</i> in the world. Owing to its rarity and biogeographical and phylogenetic importance, some parts of its habitat have been designated as a local natural monument by Hiroshima Prefecture. In this study, we described the longitudinal distribution, abundance and size structure of Gogi charr and non-native red-spotted masu salmon, <i>Oncorhynchus masou ishikawae</i>, in headwater streams flowing through a Quasi-National Park in the Gonokawa River system, to provide fundamental information regarding the conservation of this charr subspecies. The results showed that the density and relative abundance of Gogi charr decreased downstream, while the body size of age-0 Gogi charr increased. The body size of mature individuals also increased downstream, while the maturity rate decreased. The highest density of age &gt;0 Gogi charr in our streams (24.2 individuals per 100 m²) were quite higher than that of white-spotted charr <i>S. leucomaenis</i> subspp. in other regions near the southern limit of their distribution, suggesting that Gogi charr populations in our streams were in good condition, probably because the study area is relatively protected from human activities as a Quasi-National Park. However, deformed individuals of Gogi charr were found at a high frequency in a fragmented tributary (19 per total 175 individuals captured), and non-native red-spotted masu salmon tended to be numerically dominant in downstream reaches. These results indicate that our streams are valuable as a conservation area for Gogi charr, while habitat fragmentation and invasion by non-native red-spotted masu salmon are concerns.</p>