The 2016 ISC Liga Nusantara or 2016 Indonesia Soccer Championship C season is the second edition of Liga Nusantara after the Second Division and Third Division merged on 2014 season. This season is managed by competition committee of Province Association for qualification round and managed by PT. GTS in national round. The competition started in May 2016. Perseden Denpasar became champion after beating PSN Ngada 2–0 in the final.