The earliest reference to an anchorage at Tobemory was in 1549. In 1588, the San Juan de Sicilia, an Armada ship escaping from defeat in the English Channel, found refuge in Tobermory Bay, but blew up and sank. In 1788 the British Fisheries Society chose to establish a fishing station to be known as British Harbour, but the village developed commercially under its old name and the new village developed commercially, taking advantage of the increasing coastal shipping at anchor.

The first pier, "Fishermens", was built in 1814 under the direction of Thomas Telford. With the opening of the Crinan Canal (see entry) in 1817, Glasgow was now reachable in two days and steamboats started to run regular services in the 1820s, leading to a flourishing tourism business. Around the same time, large-scale emigration from the West of Scotland and the Isles took place, with chartered sailing ships - their holds roughly fitted to carry passengers - would periodically time anchor in the bay to pick up parties of emigrants sailing mainly for Canada or Australia. After the 1850s, emigrants mostly left by steamboat for Glasgow to join better regulated ships from major ports.

In 1847, the royal yacht "Victoria and Albert" anchored at Tobermory. With yachting becoming popular, another pier ("MacBrayne's") was built to serve the steamers> Such notables as Felix Mendelsson and J M W Turner followed in the wake of Sir Walter Scott and Daniell who had visited earlier in the century. The shipping magnate, Alexander Allan, built an improved estate pier at the southern end of the bay and his demolished mansion once stood in the now public park of Aros.

During the Second World War, Mull became a restricted area, with the bay now a naval base; HMS "Western Isle", under the fearsome gaze of Commodore Stephenson, the 'Terror of Tobermory', gave training to over one thousand escort vessels before they went straight into active service in the Battle of the Atlantic. The opening of the Craignure pier in 1964 began the slow decline of the deep water pier in Tobermory though goods still came into the pier until 1973 when Craignure acquired its linkspan. The last commodities to be off-loaded at Tobermory were coal and calor gas, but now goods and visitors largely arrive through the Craignure connection. The old Tobermory Pier, built for a herring fishery that never materialised, now serves growing a number of shellfish boats. A large number of yachts still come, with Tobermory Bayone of the three best harbours on the West Coast and by a considerable margin the most attractive.