Ishii began to bat lead-off in 1997. He received a Best Nine Award as the best shortstop in the Central League in 1997. He would receive this award for five consecutive years, until 2001. The Yokohama Baystars won the Central League pennant, as well as the Japan Championship Series in 1998 (38 years after their last championship in 1960). Ishii led the league in steals and hits, and received his fourth Golden Glove award at shortstop. He led the league in steals for three consecutive seasons (1998~2000).