Acheilognathus cyanostigma is an exotic fish species in Kyushu Island, being an endangered species in central Honshu Island. The distribution pattern of the exotic population in the Midori River system, Kyushu Island, Japan was examined, the species occurring at 28 low-altitude sites out of 96 sites investigated. The relationships between presence/absence of the species and environmental factors (altitude, water depth, current velocity, turbidity, river width and riverbank conditions) were analyzed using a generalized linear mixed model, riverbank conditions, water depth, turbidity and altitude having either positive or negative effects. In particular, a concrete-covered riverbed was found negatively affect distribution.