Numbers of masu salmon and Dolly Varden in streams in the Shiretoko Peninsula, location of the Shiretoko World Heritage Site in north eastern Hokkaido, appear to be declining. One concern is whether masu salmon smolts continue to migrate during July, after the existing May to June angling closure established to protect migrating smolts in eastern Hokkaido. Smolt timing and relative abundances were monitored in the Uebetsu River near the World Heritage Site from May to July during 2005–2007. Each year some masu salmon smolts emigrated during July, especially in 2005 when 82% of smolts captured were caught that month. In contrast, most anadromous Dolly Varden smolts emigrated prior to early June when stream temperatures <8°C. Mean fork lengths of smolts in both species decreased during the runs. The current fishing closure period (May to June) may be insufficient to protect masu salmon smolts in this unique area from angling.