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John was born in 1829, the son of Donald MacKillop and Ann Ferguson of old Ruisgarry then 10 Ruisgarry (Gunhill). He became a lobster fisherman and married Mary MacDonald of Claddach Illeray. They made their home in Griminish before moving to 6 Gearraidh Dubh on the Isle of Grimsay.
The book Sea-Names of Berneray tells how a searock was named after him. In the 1870s John was assisting an Admiralty Survey ship when he warned the officers about an uncharted rock. Since they were only revising existing charts they proved reluctant to believe in its existence, so were amazed when he guided the ship alongside. They duly named it MacKillop Rock.