We examined a free-living Symbiodinium species by light and electron microscopy and nuclear-encoded partial LSU rDNA sequence data. The strain was isolated from a net plankton sample collected in near-shore waters at Tenerife, the Canary Islands. Comparing the thecal plate tabulation of the free-living Symbiodinium to that of S. microadriaticum Freud., it became clear that a few but significant differences could be noted. The isolate possessed two rather than three antapical plates, six rather than seven to eight postcingular plates, and finally four rather than five apical plates. The electron microscopic study also revealed the presence of an eyespot with brick-shaped contents in the sulcal region and a narrow anterior plate with small knob-like structures. Bayesian analysis revealed the free-living Symbiodinium to be a member of the earliest diverging clade A. However, it did not group within subclade AI (=temperate A) or any other subclades within clade A. Rather, it occupied an isolated position, and this was also supported by sequence divergence estimates. On the basis of comparative analysis of the thecal plate tabulation and the inferred phylogeny, we propose that the Symbiodinium isolate from Tenerife is a new species (viz. S. natans). To elucidate further the species diversity of Symbiodinium, particularly those inhabiting coral reefs, we suggest combining morphological features of the thecal plate pattern with gene sequence data. Indeed, future examination of motile stages originating from symbiont isolates will demonstrate if this proves a feasible way to identify and characterize additional species of Symbiodinium and thus match ribotypes or clusters of ribotypes to species.