Chilika Lake, an assemblage of marine, brackish and freshwater ecosystems, on the east coast of India is a designated Ramsar site and a biodiversity hotspot. Intensive ichthyofaunal inventories and biodiversity assessments were carried out during 2000–2014 and documented 317 species belonging to 207 genera, in 88 families and 23 orders, including two endemic (Gobiidae) and one exotic cichlid species (Oreochromis mossambicus). In total, 255 collections (178 collections of previously recorded species and 77 that represent newly recorded species) were made during a post-restoration survey accounting for 80.44% retrieval of historically documented species. This paper presents an updated and comprehensive checklist of the lake’s ichthyofauna (1916–2014), which is comprised of 278 food fishes, 271 (85.49%) migratory and 46 (14.51%) are resident species indicating that the lake fishery is largely migratory species-dependent. An account of faunal characteristics for 129 commercially important species is provided. The checklist also documents 48 threatened species and 103 species under different categories of conservation status.