The atoll was named in honor of Robert Townsend Farquhar in 1824. Previous visitors had named it after Portuguese explorer João da Nova who commanded that nation's third expedition to India during which he encountered Farquhar (in the year 1504). Administration of the atoll was a grey area for many years, with both Mauritius and Seychelles claiming the right to administer it. In 1881 the authorities in Seychelles suggested Farquhar, along with several other outer islands, be administered from Victoria in Seychelles rather than from Mauritius. There were objections as the owners were based in Mauritius but after considerable argument, the owners lost their case and administration was passed from Mauritius to Seychelles.