Habitat selection of the spined loach yamato complex (Cobitidae) was investigated at the River Saigo, Fukuoka Prefecture, Kyushu Island, Japan, during both the non-spawning (from January to March) and spawning (from April to June) seasons. The study site had one pool, two riffles, and one flood region during the spawning season and is 140 m long, located 4 km stream from the river mouth. The number of yamato complex individuals was checked, and 10 physical environmental parameters were measured to assess the microhabitat in 45 quadrates. The number of individuals was counted each month, and environmental measurements were conducted four times from January to June 2010. Akaike’s Information Criterion (AICc) and Generalized Linear Model (GLM) were utilized for analysis to verify the effect of the important environmental variables on the habitat of the yamato complex. A total of 184 individuals were captured during the non-spawning and spawning seasons. The populations of yamato complex correlated positively with the water depth during the non-spawning season and with short emergent hydrophytes during the spawning season. Individuals of the yamato complex were observed in the riffle part of the river with depth during the non-spawning season and in the temporary water area with vegetation during the spawning season.