Single-stranded conformational polymorphism (SSCP) analysis of Rubisco spacer plastid haplotypes was used to assess population differentiation in the mangrove-dwelling red alga Caloglossa leprieurii (Montagne) J. Agardh. Over 1000 samples from 16 populations in northern and eastern Australia were scored with SSCP. Seven haplotypes were discovered, three of which were only found in single populations. The haplotypes formed three phylogenetically distinct lineages. A haplotype found only in north Australia (haplotype N) has closer affinities with a haplotype previously found in Japan than with any other Australian haplotypes. One haplotype (B) was dominant in northern populations and another (C) was dominant in southern populations. Haplotype A was found in geographically intermediate populations but never in high abundance ([les ] 10%). Population analysis of haplotype frequencies revealed that many populations were significantly differentiated from each other. These data indicate that populations of C. leprieurii in Australia are genetically isolated from each other, as many individual populations, probably due to limited gene flow.