The prehistoric amphioxus, described by the Scottish Government as “elusive”, was found in waters off Tankerness in Orkney.
The fish has a nerve chord down its back and is said to be regarded as a representative of the first animals to evolve a backbone.
Giant mussels with shells measuring up to 48cm (18in), were also discovered around the Small Isles and are said to have the largest sea shells in Scotland.
More than 100 specimens of the fan mussels were found around the islands, meaning the area has the largest aggregation of the fish in UK waters.
The mussels are said to have golden threads similar to human hair, which are so fine they are able to attach to a single grain of sand.
In Caithness, the country’s largest horse mussel bed was found in waters near Noss Head.
The species, known as “clabbydhhu” in Gaelic, which translates as “enormous black mouth”, are slow-growing molluscs that can live for up to 50 years.
They are said to stabilise mobile seabeds and provide a critical ecosystem for other species.
Other rare finds from the marine surveys, which covered over 2,000 square miles, included Flame Shell beds in Loch Linnhe, Argyll, as well as new communities of northern feather star, a brightly coloured species with 10 feather-like arms fanning out from a central disc.
The Scottish Government’s Environment Secretary Richard Lochhead said: “In an age where the lands of the world have been mapped out and recorded, it’s amazing how many discoveries are waiting to be found under the waves. Spanning from the weird to the wonderful, discoveries this year have included the bizarre amphioxus and the beautiful yet elusive brightly coloured flame shell.
“The waters around Scotland are rich in such fascinating biodiversity and it’s our responsibility to protect this fragile environment.
Dr Dan Barlow, head of policy at WWF Scotland, said: “By providing vital information on what lies beneath the waves, these surveys will help inform decisions on better ways to protect this important resource now and long into the future.”