Catch-and-release (C&R) angling is becoming more common worldwide for managing stream-resident salmonids but has only recently been introduced in Japan. However, few studies have examined effects of C&R regulations on fish populations through adequate experimental designs. We estimated effects of implementing a C&R regulation on stream-resident salmonids. The western part of the Agatsuma River system in Japan is a fishing area with standard regulations under which anglers can harvest white-spotted charr or masu salmon of > 15 cm total length. In contrast, the eastern part is a fishing area with a C&R regulation requiring release of all caught fish, owing to radiocesium contamination caused by a nuclear accident at Fukushima. Density and total length of stream-resident salmonids were examined in these areas in several tributaries. Fish density was significantly higher in the C&R area, whereas total length did not differ significantly between areas. Implementing a C&R regulation may be effective for conserving salmonid populations in mountainous streams.