Microsatellites are commonly used markers in population genetics and are increasingly being employed to determine population structure in phytoplankton populations. We have developed seven polymorphic microsatellite markers for the domoic-acid producing diatom Pseudo-nitzschia australis. Using these markers, thirty P. australis isolates were genotyped, 10 isolates were from Monterey Bay, California and 20 were from off the northern coast of Oregon. The number of alleles per locus ranged from two to eight and observed heterozygosities ranged from 0.11 to 0.70. All but two of the isolates were genetically distinct and initial population differentiation analysis indicated no significant differences between the Pacific Northwest isolates and the Monterey Bay isolates. Pseudo-nitzschia australis microsatellites appear to be species specific based on cross amplification tests with Pseudo-nitzschia fraudulenta (Cleve) Hasle, Pseudo-nitzschia seriata (Cleve) H.Peragallo, Pseudo-nitzschia pungens (Grunow ex Cleve) and Pseudo-nitzschia multiseries (Hasle) Hasle. Published by Elsevier GmbH.