Trichodesmium tenue Wille (1904) was examined using transmission electron microscopy to determine the role of carbohydrate, phosphorus, and nitrogen storage in buoyancy regulation. Carbohydrate storage area (mean = 2.06 ± 0.61 [SE] μm2; 6.62% of total cell area) in negatively buoyant colonies (NBCs) was significantly higher (P < 0.001) than in positively buoyant colonies (PBCs) (mean = 0.38 ± 0.06 μm2; 0.73%). Distinct diel periodicity of carbohydrate content was found in NBCs demonstrated by an increase from darkness to afternoon. Polyphosphate content was significantly higher (P < 0.001) in NBCs, with a mean of 0.44± 0.10 μm2 (1.54%), as compared to PBCs, with a mean of 0.14 ± 0.05 μm2 (0.24%). Polyphosphate content increased in NBCs from morning to evening, and PBCs had a 10% decrease from morning to afternoon. Calculations indicated that averaged effects of polyphosphate on increased cell density is approximately 20% of that from carbohydrate accumulation. Density contribution due to ballast weight of carbohydrate and polyphosphate indicated that NBCs were 12 times more dense than PBCs. Mean area of cyanophycin granules (N storage) was not significantly different between PBCs and NBCs. In conclusion, Trichodesmium tenue can regulate buoyancy by carbohydrate ballasting similar to that noted in limnetic cyanobacteria. Polyphosphate storage and possibly nitrogen storage products play a significant role in buoyancy regulation.