Zooxanthellae are phototrophic dinoflagellates that occur as endosymbionts in many marine invertebrates. Because traditional biological methods have not provided useful schemes for zooxanthella identification and classification, the natural history of zooxanthella symbioses is poorly known. We have apphed molecular genehc methods to zooxanthella taxonomy. Small ribosomal subunit RNA (ssRNA) genes can be rapidly obtained from small amounts of symbiotic (non-cultured) algae by gene amplification using the polymerase chain reaction. Different Symbiodinium-like zooxanthellae are then identified by digesting the amplified DNA with restriction enzymes. A sample of 16 cnidarian host species yielded 6 distinct Symbiodinium ssRNA genes: different Hawaiian corals harbored dfferent algae, but different individuals of the same coral species harbored indistinguishable algae. The corals Pocillopora damicornis and P. meandrina appear to contain a mixture of 2 zooxanthella ssRNA genes; other hosts exhibited a single zooxanthella genotype. The same algal genotype occurs in taxonomically dissimilar hosts.