We report the characterization of six new microsatellite loci for the toxic marine dinoflagellate Alexandrium tamarense (North American ribotype), using 56 isolates from a range of locations. The numbers of alleles per locus ranged from five to nine and gene diversities ranged from 0.041 to 0.722. We tested primers for these six loci on other A. tamarense ribotypes and on other Alexandrium species; the results suggest that the primers are specific to A. tamarense isolates belonging to the North American ribotype. © 2006 The Authors.