We show the first conclusive evidence that Melitasphaeridium choanophorum, a dinoflagellate cyst species until recently considered extinct, is still living in the northern Gulf of Mexico. This suggests the Gulf of Mexico may have acted as a refugium for some warm-water dinoflagellates during past glaciations. Melitasphaeridium choanophorum can be considered a living fossil because cysts with cell contents were found among 15 of the 39 surface sediment samples analyzed from the northern Gulf of Mexico, and from five of 12 samples from a dated core (1962–1997). Melitasphaeridium choanophorum comprises a minor component of the total dinoflagellate cyst assemblages, with a maximum of 1.4% or 15 cysts g−1. It was found in surface sediments with overlying sea-surface temperatures of 16.6 to 31.2 °C (winter and summer), and summer sea-surface salinities of 21.0 to 31.7 psu. The relationship of M. choanophorum with modern sea-surface conditions can be used to infer past oceanographic conditions.