Effective population size (N_e) determines the rate of genetic drift and the relative influence of selection over random genetic changes. While free-living protist populations characteristically consist of huge numbers of cells (N), the absence of any estimates of contemporaryN_eraises the question whether protist effective population sizes are comparably large. Using microsatellite genotype data of strains derived from revived cysts of the marine dinoflagellatePentapharsodinium daleifrom sections of a sediment record that spanned some 100 years, we present the first estimates of contemporaryN_efor a local population in a free-living protist. The estimates ofN_eare relatively small, of the order of a few 100 individuals, and thus are similar in magnitude to values ofN_ereported for multicellular animals: the implications are thatN_eofP. daleiis of many orders of magnitude lower than the number of cells present (N_e/N∼ 10⁻¹²) and that stochastic genetic processes may be more prevalent in protist populations than previously anticipated.