A method for the rapid identification of plastid haplotypes in red algae is presented. This method is based on single-stranded conformation polymorphism (SSCP) to detect variation in DNA sequence of PCR-amplified plastid-encoded ribulose bisphosphate carboxylase/oxygenase large and small subunit intergenic spacer. The method detects variation within a population of the mangrove red alga Caloglossa leprieurii from New South Wales, Australia. Three haplotypes (plastid variants) were easily scored in our samples, and a spatial variation of haplotypes within the intertidal is suggested. This method also reveals maternal inheritance of plastids in crosses between isolates of Bostrychia radicans and in multiple crosses between isolates of B. moritziana. Fluorescence microscopy shows that plastids are contained within the spermatia of these species and that bi- or paternal inheritance of plastids is possible. SSCP is a simple and rapid method for the detection of plastid variation (haplotypes) within populations of red algae that should also be applicable to brown seaweeds.