We examined the selectivity of spawning habitat for shishamo smelt (Spirinchus lanceolatus) in December 2001 at pools and riffles of the Pon-warui stream, located in southern Hokkaido, Japan. We analyzed the sampling sites of fertilized shishamo smelt eggs in relation to environmental variables using princi-pal component analysis and ANOVA. The results showed that the eggs were dis-tributed to the pools with shallow (2-22cm), slow moving water (-0.07-0.10m/sec) and fine substrate (sand: particle size<2mm). The eggs are normally dis-persed downstream from the spawning ground (riffle or glide) by the stream cur-rent and should settle down against the bank of pools, highlighting the importance of preserving the pool-riffle sequence throughout the river system.