Dr. Salim Ali died in Bombay at the age of 90 on 20 June 1987, after a protracted battle with prostate cancer. In 1990, the Sálim Ali Centre for Ornithology and Natural History (SACON) was established at Coimbatore by the Government of India. Pondicherry University established the Salim Ali School of Ecology and Environmental Sciences. The government of Goa set up the Salim Ali Bird Sanctuary and the Thattakad bird sanctuary near Vembanad in Kerala also goes by his name. The location of the BNHS headquarters in Mumbai was renamed as "Dr Salim Ali Chowk". In 1972, Kitti Thonglongya discovered a misidentified specimen in the collection of the BNHS and described a new species that he called "Latidens salimalii", considered one of the world's rarest bats, and the only species in the genus "Latidens". The subspecies of the rock bush quail ("Perdicula argoondah salimalii") and the eastern population of Finn's weaver ("Ploceus megarhynchus salimalii") were named after him by Whistler and Abdulali respectively. A subspecies of the black-rumped flameback woodpecker ("Dinopium benghalense tehminae") was named after his wife, Tehmina, by Whistler and Kinnear. Salim Ali's swift ("Apus salimalii") originally described as a population of "Apus pacificus" was recognised as a full species in 2011 while "Zoothera salimalii", an undescribed population within the "Zoothera mollissima" complex, was named after him in 2016.