Energy dispersive X-ray microanalysis (XRMA) in a scanning electron microscope (SEM) was used as a method to measure elemental silicon (Si) and phosphorus (P) in dinoflagellate cysts. Cysts were prepared by quick deep freezing and then freeze-drying, thereby avoiding the addition of preservatives. Cysts of Ceratium hirundinella collected from Lake Erken, Sweden and Esthwaite Water, UK, and Ceratium furcoides collected from Esthwaite Water, were analysed and compared. The hypothesis that cysts are able to assimilate P during dormancy was tested in the laboratory by incubating newly collected cysts of C. hirundinella in medium with and without phosphate. The analyses showed that there was no difference in P content between C. hirundinella and C. furcoides, suggesting that P content reflects differences in physiological status rather than species. C. hirundinella had a significantly higher Si content than C. furcoides, which agrees with earlier studies. Comparison of cysts of C. hirundinella from different years – 1995 (stored for 1 year), 1996 and 1997 – showed that the P content in cysts from 1995 was higher than that in cysts from the following 2 years, which indicates either that P was higher during encystment in 1995 or that cysts accumulated P during dormancy. The P uptake experiment showed a very slightly, but significantly, higher, P content in cysts incubated in P-rich medium.