Ayumodoki (Parabotia curtus), a critically endangered loach, survives only in three locations in western Japan. Its population in Yagi, Kyoto Prefecture, went extinct in the wild in the 1990s but has been maintained in captivity for over 40 years. This study investigated fish fauna in the areas including the former and nearby current habitats primarily using environmental DNA metabarcoding. We detected 41 freshwater fish species from 26 sites, but P. curtus was found only in its known habitat in Kameoka. However, the species composition suggests that re-establishing the population in the Yagi former habitat is feasible if spawning habitats and migration routes are improved. Adequately maintaining the captive population and enhancing the local environment are crucial for successful reintroduction.

The native range of “Type I” mitochondrial DNA (mtDNA) of the dojo loach (Misgurnus anguillicaudatus complex), originating from M. sp. Type I sensu Okada et al. (2017), is found only in Japanese native dojo loach populations on the eastern Pacific and central-north Japan Sea regions of Honshu Island. However, a stand-alone distribution of Type I mtDNA was recently reported from a few individuals in a single dojo loach population in Nagoya City, Aichi Prefecture, located in central Honshu Island. Genetic analyses on 54 individuals (out of 81 collected from the population) were conducted to clarify the strict phylogenetic position of Type I mtDNA and the genetic population structure. Genetic screening and sequencing analyses targeting the Cytb gene region revealed a single common Type I haplotype in only four individuals. Although the independent phylogenetic status of the haplotype among Type I haplotypes from the entire native range was confirmed, it was clustered with known Type I subclades detected from the west side of the Fossa Magna region. Such genetic independence and its relationship to geographical proximity indicated that the haplotype was native to that region. Nuclear DNA analysis targeting the IRBP2 and RAG1 gene regions revealed that most individuals were hybrids among three groups comprising the detected mtDNA (Type I and Types IIa and IIb, originating from Japanese native and Chinese clades of M. anguillicaudatus). Four individuals carrying Type I deviated significantly from random mating with individuals carrying other mtDNA types, and two individuals with notable morphological characteristics of M. sp. Type I (including genetic factors associated with M. sp. Type I in both mitochondrial and nuclear DNA) indicated that M. sp. Type I had maintained its genetic integrity in the presence of the other two groups.

Diet and habitat characteristics of juvenile stages of the endangered sculpin Cottus reinii were investigated in eight rivers flowing into Lake Hinuma, a brackish water lake in Ibaraki Prefecture, eastern Japan, from April to September 2020. Juvenile C. reinii fed mainly on aquatic insects, such as chironomid, baetid, simuliid and trichopterid larvae, and gammaridean amphipods. A generalized linear mixed model based on occurrence/non-occurrence data in the former with a number of environmental variables at sampling sites in eight rivers in May and June (upstream migration period) and August and September (post-migration) revealed that lower weir height, shallower water depth, lower water temperature, greater current velocity, and greater coverage by submerged vegetation were the most significant determinants of juvenile occurrence.

When selecting founders of endangered species for ex situ conservation, it is necessary to acquire sufficient individuals so as to ensure the genetic diversity of the ex situ population, while taking into consideration the impact of removing founders from the in situ population. Surveys for population estimation by removal method were conducted for two Cobitis species in November 2019. For each estimation, a population was surveyed 5–8 times using dip nets to remove captured individuals, the hierarchical Bayesian model being used to estimate the number of individuals in the population. The Cobitis takenoi population was estimated 500–5,305 (95% CI) individuals, and the Cobitis striata hakataensis population, 249–1,601 (95% CI) individuals. The number of individuals selected to be founders was based on the lower limit of the 95% credible interval of the estimate, thereby minimizing the impact on the in situ population. This established protocol was considered to be a model case for securing future ex situ conservation populations.

Using mitochondrial DNA cytochrome b region nucleotide sequences, we investigated the phylogeographical structure of Tanakia lanceolata, which inhabits the Tokai region of central Honshu, Japan. As a result, we found one non-native haplotype (native distribution in the Kinki region) and 32 native haplotypes in the Tokai region. The non-native haplotype was only found in the Shin River system in Aichi Prefecture. Therefore, it is suggested that artificial introduction from other regions is limited. Among the haplotypes included in the native lineage, one haplotype was widely distributed in the Tokai region, while 31 haplotypes were endemic to one river system or neighboring river systems. The analysis of molecular variance (AMOVA) showed genetic differentiation between river systems. We propose to consider each river system as conservation units.

Nine specimens (126.9–194.6 mm standard length) of the morid Laemonema rhodochir Gilbert, 1905, previously recorded in the North Pacific Ocean from the Hancock Seamount, Hawaiian-Emperor Seamount Chain, Hawaiian Islands, Kyushu-Palau Ridge, and Taiwan, were collected from the Koko, Yuryaku, and Colahan Seamounts (Emperor Seamount Chain) and Sagami Bay, representing the first record from each locality and northernmost range extension of the species (Sagami Bay, off Zushi City, Kanagawa Prefecture, Japan, ca. 35˚15′N). Re-examination of the type specimens of L. rhodochir and L. palauense supported a previous view that the former species is the senior synonym of the latter.