Carbohydrates are an important organic compound class in seawater and play an active role in the biogeochemical cycling of organic carbon and trace elements in the ocean, but are poorly characterized. To better understand the sources and role of carbohydrate species in marine environments, the concentrations and fluxes of particulate carbohydrates (CHO), total acid polysaccharides (APS), uronic acids (URA), phytoplankton composition and bacterial production were measured in the Gulf of Mexico in 2000 and 2001. A strong positive correlation between APS concentration and cyanobacteria abundance was found in 2000. In 2001, prymnesiophyte abundance correlated well with both concentrations of APS and URA. Bacterial production data, measured simultaneously in 2001, showed significant positive relationships with particulate organic carbon (POC), CHO, APS and URA concentrations, respectively. The average fluxes out of the euphotic zone of CHO, APS and URA in 2000 were 8.1, 1.3, and 0.7 mg C m⁻² d⁻¹, respectively. In 2001, the average fluxes of CHO, APS and URA were about 3 times higher than those in 2000, which was a time of lower nutrient concentrations, indicating that the fluxes of carbohydrate species are related to the nutrient status and phytoplankton composition. The results suggest that APS in the upper water column can be produced by cyanobacteria, prymnesiophytes, and heterotrophic bacteria. Most importantly, our data indicate that APS and CHO compounds are more resistant to biological degradation than other organic compounds, suggesting that the role of CHO compounds in carbon cycling in the ocean is more complex than previously thought.