Zonation of macroalgae in the intertidal zone has been well documented. However, studies of zonation of macroalgae have predominantly examined the distribution of different species rather than the distribution of variants within a species. This study investigated the spatial variation of plastid haplotypes of the mangrove red alga Caloglossa leprieurii (Montagne) J. Agardh at a site in eastern Australia and tests for physiological differences (growth, photosynthesis) between those haplotypes. RUBISCO spacer plastid haplotypes were scored using single-stranded comformational polymorphism, and the population structure at two sites was examined using a nested sampling design comparing between sites, among transects within sites, and among quadrats within transects. Growth rates at various salinities and light intensities and the photosynthesis–irradiance curves of the three main haplotypes were compared. The two sites showed a high degree of genetic differentiation across a short distance, suggesting limited gene flow. The distribution of haplotypes was patchy and did not reflect a zonation pattern along the intertidal gradient. The three haplotypes were physiologically differentiated with haplotype A, with a lower growth rate and a lower photosynthetic efficiency at higher light intensities. There is some evidence of physiological differentiation between life history phases in C. leprieurii with sporophytes having a higher growth rate than females under most conditions. Our results suggest a correlation between our culture results and our population data. Haplotypes (haplotype A) and life history phases (gametophytes) with lower performance (growth and photosynthetic efficiency) under our culture conditions were correlated with a minor representation in the field. This is the first study to integrate population-level data with physiological parameters toward an understanding of the distribution and relative abundance of red algal genetic variants.