Since January 2015, Japan has restricted harvesting of tuna weighing less than 30 kg (juvenile tuna), in accordance with Western & Central Pacific Fisheries Commission agreements. With the goal of re-attaining historical intermediate values of 43,000 tons of tuna resources by 2024, there is now an upper limit of 4,000 tons on the annual catch of juvenile tuna. Tuna fishing in Japan is performed by purse seine or set-net fishing, and quotas are allocated for each. Quotas for set-net fishing in Japan are allocated among six nationwide blocks. Set-net fishing is a passive method in which fishermen cannot control the amount or fish species that enter the nets. The catch in 2015 in the block that includes the coastline near Hakodate City exceeded quotas for juvenile tuna, so in June 2016 fisheries cooperative association implemented a 14-days fishing holiday with the goal of resource management. However, the resource conservation effects of such fishing holidays are unknown. A better approach for appropriate resource conservation would be cessation of fishing after the number of juvenile tuna entering set-nets exceeds a predetermined level. We therefore attempted juvenile tuna identification by attaching floating echo sounders to set-nets and analyzing the accumulated sonar data. We found that focusing on the periodicity of time-series sonar data allows such identification.