Studies on the morphology, reproductive compatibility, life cycle and molecular phylogeny of the euryhaline red alga Caloglossa provide insights into the speciation events and biogeographic patterns. The C. leprieurii complex is separated into three morphotypes based on the number of cell rows at nodes and the blade width. The three morphotypes are reproductively incompatible with each other, and furthermore many mating groups are recognized within the morphotypes. Incomplete reproductive isolation is occasionally seen between geographically distant mating groups, whereas no sexual compatibility occurs between sympatrically or parapatrically distributed mating groups. In the molecular phylogenetic analyses, the C. leprieurii complex is resolved as two clusters that phenotypically correspond to the single and multiple cell row types, respectively. The strains belonging to the same mating group are closely related to each other, without exception, while the mating groups showing incomplete reproductive reactions do not always make a clade. The genetic distance is generally not correlative to the geographic distance, and this is also suggested by the morphological data and crossability. These results indicate that allopatric speciation has frequently occurred in this species complex, although there is some evidence of long-distance dispersal.