The fossil dinoflagellates Spiniferites bentorii, S. mirabilis, and S. membranaceus are known to inhabit recent sediments and are often used to reconstruct past sea‐surface conditions. However, information on their corresponding motile cells has been rare. We isolated single cysts resembling these fossil species from China and France to yield Gonyaulax spinifera‐like cells. Gonyaulax strains were also established from Viet Nam and South Korea by isolating single cells. Both cysts and cells were examined by light and scanning electron microscopy, and their LSU rRNA genes were sequenced. A new Gonyaulax species, G. carbonell‐mooreae, was obtained from S. bentorii‐like cysts and considered the equivalent of Spiniferites bullatus, dating back to the Campanian. Gonyaulax kunsanensis was related to S. mirabilis‐like cysts. A typical S. membranaceus cyst from France yielded cells resembling G. lewisiae but shared only 75% similarity in LSU rRNA gene sequence with those from South Korea. Molecular phylogeny revealed that the pronounced apical boss is systematically significant, whereas the presence of intergonal processes is insignificant. Two ASVs of 18S rRNA V4 region were respectively identified as G. kunsanensis and G. lewisiae from the Tara Oceans metabarcoding data. Gonyaulax kunsanensis has a wide distribution in the Pacific, Indian, and Atlantic Oceans, but G. lewisiae has a restricted distribution. One strain of G. kunsanensis was examined for yessotoxin content using liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS), but no detectable amounts of toxins were observed. Our results uncover the hidden diversity within the G. spinifera species complex and stress the significance of cyst morphology in the taxonomy of Gonyaulax.