Regional and local habitat factors affecting the distribution and abundance of Japanese eel (Anguilla japonica) were systematically analysed in 123 reaches of 21 stream systems in south‐western Japan, with particular attention paid to human habitat modification, such as artificial barriers and concrete revetment. The density of Japanese eel decreased upstream, and they were absent from the upper reaches of each stream system. The upper limits of their distribution were explained by the distance from the sea and the channel gradient, rather than barriers. However, the number of barriers had the highest explanatory capacity for the upstream decline in abundance of small eels (<40 cm in total length). Analyses of the relative importance of regional and local habitat factors showed that the number of barriers (regional factor) was more important than local habitat factors in determining small eel abundance, whereas regional and local habitat factors (e.g. concrete revetment or cover habitat) were similarly important for large eel abundance. These results suggest that: (i) barriers are not a major factor limiting the distribution (presence/absence) of the Japanese eel in the streams studied; (ii) barriers can substantially decrease the abundance of young eels; and (iii) as eels grow older and larger, local habitat factors, such as bank conditions and cover, become more important in determining their abundance. The results for the relative importance of regional and local habitat factors suggest that in habitat restoration for the Japanese eel, priority should be given to mitigating barrier effects. The improvement of longitudinal connectivity to facilitate colonization by young eels is primarily needed for a more efficient use of the existing carrying capacity of streams. The improvement of local habitat conditions to increase the carrying capacity should be conducted in stream reaches free from barrier effects.
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