© 2016 John Wiley & Sons, Ltd. All rights reserved. Japanese inland fisheries and aquaculture produced 34×103 and 39×103 t in 2011, representing only 0.7 and 4.5% of their corresponding total marine production. Salmonids and ayu Plecoglossus altivelis altivelis are the main fish products taken from rivers, and the main products from lakes are shellfish and Japanese pond smelt Hypomesus nipponensis. Japanese eel Anguilla japonica, common carp Cyprinus carpio and crucian carp Carassius spp. are caught in both rivers and lakes. The principal targets of aquaculture are A. japonica, salmonids, P. a. altivelis and C. carpio. Japanese inland fishery production has decreased to c. 25% of the highest production in 1978 as a result of environmental deterioration, epidemics such as bacterial coldwater disease and koi herpesvirus, and predation by invasive alien fishes and waterfowl. Active seed stocking is conducted to supplement natural reproduction and to facilitate recreational fishing, which is important for the local economy. Removal of invasive alien fishes and habitat restoration have been simultaneously conducted to increase the sustainability of Japanese inland fisheries.