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Cysts belonging to the benthic dinoflagellate Bysmatrum subsalsum were recovered from palynologically treated sediments collected in the Alvarado Lagoon (southwestern Gulf of Mexico). The cysts are proximate, reflecting the features of the parent thecal stage, and their autofluorescence implies a dinosporin composition similar to the cyst walls of phototrophic species. This finding is important for our understanding of B. subsalsum life cycle transitions and ecology. Encystment may play an important role in the bloom dynamics of this species as it can enable the formation of a sediment cyst bank that allows reinoculation of the water column when conditions become favorable. This is the first report of a fossilized cyst produced by a benthic dinoflagellate recovered from sub-recent sediments.