Many fossil forms of dinoflagellates are known -- approximately 2000 species in 425 genera. These are almost never fossils of the organism in its active state, but fossils of cysts, which enable dinoflagellates to survive periods when their environment dries up. One such class of cyst are called "hystrichospheres", which are spiny balls with a long fossil record. Because dinoflagellates are sensitive to changes in ocean temperature, salinity, and nutrient levels, the dinoflagellate species that are present in a sediment sample are often used to determine the environmental conditions at the time and place that the sediment was deposited.
The fossil record of the group may extend into the Precambrian. Spherical organic-walled microfossils known as acritarchs, some of which may be dinoflagellate hystrichospheres, first appear in rocks about 1.8 billion years old. However, acritarchs lack a characteristic dinoflagellate feature, the archaeopyle or excystment pore through which the dinoflagellate exits the cyst; they also lack the cingulum groove characteristic of many dinoflagellates. Various other algae can form cysts that look superficially similar. Exactly what the acritarchs were is not known with certainty; they probably included a number of clades of eukaryotic algae, and are thus a "form taxon," including all those spore-like fossils which have not been conclusively assigned to another group.
The earliest known fossil that might possibly be a true dinoflagellate, Arpylorus antiquus, is from the Silurian Period, about 400 million years ago. Dinoflagellate fossils are rare in the Paleozoic, but there are many fossils from the Late Triassic onward. There is, however, geochemical evidence for the presence of dinoflagellates in the early part of the Paleozoic and late Precambrian, even though no cysts are known. This comes in the from of dinosteranes, chemical products derived from dinosteroids. Interestingly, the dominant modern coral group, the Scleractinia, took off at about the same time the dinoflagellates did. The zooxanthellae in these corals are dinoflagellates, and it is suspected that there may be a relationship between their diversifications.
Want more data on acritarchs? You can search the UCMP micropaleontology type collection using "acritarch" as a search-term.
You may view a chart of the abundance of different taxa of dinoflagellates through time, created by Andrew MacRae at the University of Calgary.