The group said it was attracted to invest because of Aquapharm's fermentation technology, which means it can develop pharmaceuticals and industrial products, including pigments and antioxidants for the nutraceutical market, without the use of petrochemicals.
The money comes from a £25m capital fund, which makes up Tate & Lyle Ventures, and is used to invest in "high growth" companies in the fields of renewable ingredients, food technologies, and renewable resources, such as biomaterials and biofuels.
Other companies in the €5.97m deal include Amsterdam based venture capital fund, Aescap Venture.
Co-investors include Scottish Enterprise, NESTA Investments and Argyll and the Islands Enterprise (AIE), with Tate & Lyle as the principle investor.
Managing partner for Tate & Lyle Ventures, Dr Simon Barnes, said: " Aquapharm has an excellent ability to develop natural marine-derived ingredients for a wide range of functional food applications and nutraceuticals.
"Aquapharm's focus on the sustainable production of ground-breaking bio-ingredients and the advancement of fermentation technology enjoys an excellent fit with our fund strategy."
Aquapharm chief executive, Dr Andrew Mearns Spragg, said: "Completing this new investment is recognition by venture capital of the exciting advances made by the company over the past 3 years in the areas of anti-infective development and novel ingredients for functional foods and cosmeceuticals.
"It is another confirmation of the potential economic benefits that marine biotechnology holds for the development of new innovative natural products for health and wellbeing."
Aquapharm develops new bioactive compounds derived from marine micro-organisms.
Using its fermentation technique it has been able to culture previously uncultivable microbes from collected samples and has built a substantial library of over 6,500 marine bacteria and fungi.
The firm has developed new chemical entities with interesting properties and immediate market application, including pharmaceutical compounds such as new antibiotics to tackle MRSA, anti-oxidants and anti-ageing compounds as well as carotenoids, polymers, oligosaccharides and essential fatty acids.
Aquapharm is located near Oban, Scotland, within the facilities of the European Centre for Marine Biotechnology (ECMB).
The company currently employs a team of 15 full-time staff.
The first investment for Tate & Lyle Ventures came in January with food diagnostics firm Lumora.
Tate & Lyle reported a strong full year 2007 and confirmed that continued sales growth was being generated by the food and industrial ingredients businesses, which achieved operating profit growth of 36 per cent on the prior year.
Overall the group reported sales from continuing operation of £3.81bn (€5.6bn) for the 12 months ending March 31, up from £3.46bn (€5.09) the previous year.
Operating profit was £333m (€490m).